Just source the Tcl file and use the 'unwrap' procedure. eduRe: Question about equilibration. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. Kisiela and Hovhannes Avagyan and Della J. /night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum stay: 2 night(s) Book online - Book holiday rental 11131246 with Vrbo. Sarah Keller Professor. You should simulate it in explicit water (or try one of the implicitCompiling NAMD 2. rtf" and "par_all36_prot. Choose File -> Save Coordinates. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected] on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallConvert solvated CHARMM PDB + PSF to Amber. washington. uiuc. Proteins 78, 2506–2522 [PMC free article] [Google Scholar] > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Hemostasis in vertebrates involves both a. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. Gianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. In reply to: Gianluca Interlandi: "Compiling NAMD 2. Eric Klavins Professor. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. There have been over 180 downloads and no complaints so far. Re: Help building a desktop for namd. edu> > wrote: > are other people also using those GPUs? > >In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. at 298. Location info. From: Gianluca Interlandi (gianluca_at_u. , and Thomas W. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. washington. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. washington. Hope the video helps, but now I'm embarrassed. Justin Kollman Professor. 20-23 2012)<br><br>2001 May/2002 September: Master in Tourism Management - Academy of Trade and Tourism, Trento, Italy (1900 hrs). FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated lectin domain (LD) that binds mannose on the. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. washington. From: Gianluca Interlandi (gianluca_at_u. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. View all 11 amenities. washington. 97 pN*nm = 1 Kcal/molOn Wed, Nov 26, 2014 at 04:06:03PM -0800, Gianluca Interlandi wrote: > Dear vmd list, > > I noticed that I get slightly different results when I measure the > distance between two atoms using "measure bond" vs by measuring the length > of the vector between the two atoms. I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Rooms and beds. washington. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. washington. washington. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. uiuc. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and. Gianluca Interlandi [email protected] orcid. Bidet · Toilet · Shower. washington. MyGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. , "not (water or ions)" GianlucaRe: DCD. Try copying it again from where the simulation was run. 7 ns/day, which seems decent given the system size. Bathrooms: 1. {Gianluca Interlandi and Svava K Wetzel and Giovanni Settanni and Andreas Pl{"u}ckthun and Amedeo Caflisch}, journal={Journal of molecular biology}, year={2008},. g. . washington. I > attach a plot of a constant velocity simulation where I'm pulling two > proteins apart. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping. Hope the video helps, but now I'm embarrassed. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". 15 K 1 KT = 2. Search for: Main Menu. Education/training Institution and location Dates attended Degree Conferred Field of study Interlandi G, Thomas WE. uiuc. washington. We are building a smaller cluster though in the lab and will test the scalabilityGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. What can be the possible cause for this or does it happens naturally> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. The otherGianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. From: Gianluca Interlandi (gianluca_at_u. VMD-L Mailing List. Search for: Main Menu Author Summary A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive (orthosteric) mechanism. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. University of Washington Department of Bioengineering. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. washington. washington. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. 6 version, although I am not running the cluster at full load yet. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. 1002/prot. edu> wrote: > Hi, > > Can the current version of NAMD be used together with the new CHARMM36 force > field? The parameter files are "top_all36_prot. washington. I know the lack of treatment of the hydrophobic part but the point In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Stereo system. 7b4 is thatRE: DCD. edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass"In reply to: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ attachment ] If that's the only force you are applying to the system, then that is your external work. , heavy winds caused a tree along the Burke-Gilman Trail to break in half, nearly striking a cyclist and pedestrians. Facebook gives people the power to share and makes the world more open and connected. unizh. edu on behalf of Gianluca Interlandi [gianluca_at_u. washington. From: Gianluca Interlandi (gianluca_at_u. , and Thomas W. washington. Chemistry. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. washington. uiuc. washington. In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. 7b1 on NCSA Abe. I would be > happy if somebody could point me out to some scripts which help me performRe: Help building a desktop for namd. com) Date: Thu Apr 07 2011 - 14:21:33 CDT Next message: Gianluca Interlandi: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Gianluca Interlandi: "Re: Abe versus Lincoln" Next in thread: Gianluca Interlandi: "Re:. From: Victor (ovchinnv_at_gmx. washington. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. She joined Schiller DuCanto & Fleck LLP in 1999 as a law clerk and became partner with the firm in 2009. You should simulate it in explicit water (or try one of the implicitOn Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. > > Forget about creating a pdb file. Re: query about wrapped coordinates. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. Write a review. . edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"From: Gianluca Interlandi (gianluca_at_u. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. I am > using the option "wrapAll on". Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. washington. . washington. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. Don't take my word that this works. From: Gianluca Interlandi [gianluca_at_u. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. Fwd: Installing NAMD on windows. Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. Previous message: Gianluca Interlandi: "stepspercycle" In reply to: Gianluca Interlandi: "stepspercycle" Next in thread: Gianluca Interlandi: "Re: AW: stepspercycle" Reply: Gianluca Interlandi: "Re: AW: stepspercycle" Messages sorted by: [ attachment ] No idea where you were looking, but this parameter is still fundamental for. Correspondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. upenn. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. 1 on it using Legacy Bios and a. edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. Gianluca Interlandi, research assistant professor, and Wendy Thomas, professor: Antibody Dependent Enhancement, a type of immune system backfiring that causes increased infection in cells, is likely responsible for disappointing results on experimental vaccines for SARS and MERS, and. From: John Stone (johns_at_ks. edu > <mailto:gianluca_at_u. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. washington. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!One Bedroom Apartment, Sleeps 3 - £83 avg. Sorry for posting it here, but maybe somebody might have tried it, too. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. washington. 7b1 on NCSA Abe. com) Date: Wed Sep 18 2013 - 14:48:11 CDT Next message: Gianluca Interlandi: "Re: Open VMD from a remote host" Previous message: John Stone: "Re: Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Gianluca. }, author={Dagmara I. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. From: Gianluca Interlandi (gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. Check the NAMD log! Any errors or warnings?"wrapAll on" with a complex. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). From: Gianluca Interlandi (gianluca_at_u. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. 1 the measure command of VMD can also > calculate the energy: > > energy energy_term atom_list [parameters] [options]: Returns the > specified energy term for a given set of atoms. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi <gianluca_at_u. edu Subject: Re: namd-l: DCD Load your psf+dcd into VMD. Academic ProgramsFrom: Gianluca Interlandi (gianluca_at_u. washington. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated le. , "not. Anderson: "Re: rlwrap problem on" In reply to: Frank Barry: "rlwrap problem on" Next in thread: Gianluca Interlandi: "Re: rlwrap problem on" Reply:. You should simulate it in explicit water (or try one of the implicitIn reply to: Gianluca Interlandi: "What, if no temperatue control specified?" Messages sorted by: [ attachment ] Hi! A technical question. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. washington. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). washington. washington. The simulations were not performed at constant velocity > but at constant force. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> wrote: > Roy, > > I think that you are confusing two things. washington. 7 ns/day, which seems decent given the system size. washington. Rachel Tsai 1 , Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. edu> wrote: > Hi Fatemeh, > From: Gianluca Interlandi (gianluca_at_u. 6 ns/day for a 100k atom system with roughly those same parameters (and. It's > slightly faster but still not that much faster than running on 16 CPU cores. Just source the Tcl file and use the 'unwrap' procedure. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. Next in thread: Gianluca Interlandi: "Re: NAMD 2. Cheers! If you are looking for Virtual General Counsel, please go to: out professional insights posted by Isabella Interlandi, Attorney at Law, Legal adviser, UNSC 1540 Committee former Expert, Customs legislation and procedures. edu) Date: Wed May 16 2007 - 14:43:41 CDT Next message: Ayşe Özlem Sezerman: "System charge" Previous message: Peter Freddolino: "Re: Minimization" In reply to: Viswanadham Sridhara: "How to unsubscribe ?" Messages. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. (did you see if any hunk failed?) Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. 85. > Le 2015-07-16 17:20, Gianluca Interlandi a écrit : >> Also, apropos documentation. (Oct-Nov 1997) Spanish: Fluent written and spoken German: Basic Knowledge WORK EXPERIENCE 2019 October: Founder Host. 26055 Abstract The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallNext in thread: Gianluca Interlandi: "Re: NAMD 2. " >> Could a small damping coefficient lead to such errors? If so, what would >> be the scenarioGianluca On Sun, 30 Aug 2009, Axel Kohlmeyer wrote: > On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: >> Thank you Mike for sharing your information. edu) Date: Thu Nov 02 2006 - 13:55:24 CST Next message: Ugur Akgun: "ABF on a single molecule" Previous message: Al-Rawi, Ahlam: "external force" In reply to: Al-Rawi, Ahlam: "external force" Next in thread: Gianluca Interlandi:. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallmargin errors. edu> > wrote: > Roy, > > I think that you are confusing two things. On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. >Re: Vibrational mode analysis. Sarah Keller Professor. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. edu Search for more. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Gianluca Interlandi composed on 2017-01-23 13:40 (UTC-0800):. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the charmm++. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. I would be > happy if somebody could point me out to some scripts which help me performDCD. MyFrom: Gianluca Interlandi (gianluca_at_u. washington. Neil King Assistant Professor. Deadline is this Friday (or in three > months). washington. Search 214,979,228 papers from all fields of science. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. However, using monoclonal antibodies specific for the mannose-binding Escherichia coli. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. From: Stern, Julie (jvstern_at_bnl. washington. edu> wrote: > A few of the simulations aborted with the following message: >> "ERROR: Atoms moving too fast; simulation has become unstable. edu]Reply All Saturday,. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. washington. washington. From: Gianluca Interlandi (gianluca_at_u. On Tue, Jul 10, 2012 at 1:14 PM, Gianluca Interlandi < gianluca_at_u. Gianluca has 2 jobs listed on their profile. washington. From: Gianluca Interlandi (gianluca_at_u. washington. Comparative controls consisted of FocH (high affinity with and. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? Next in thread: Gianluca Interlandi: "Re: NAMD 2. In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" INVENTING THE FUTURE OF MEDICINE. Gianluca Interlandi Research Assistant Professor. I doubt that there is a way to have NAMD output theGianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>@article{Kisiela2015EffectOM, title={Effect of mAb926 and mAb475 on biofilm formed by E. Gianluca, Yes, I think that a higher damping constant will indeed slow down conformational sampling. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. I'm > not sure whether the CHARMM program can read. > However, topology and parameters for water and ions are. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. From: Mitchell Gleed (aliigleed16_at_gmail. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. I was recording the energies once every 100 steps. Hemostasis in vertebrates involves both a cellular and a protein component. edu> wrote: > Roy, > > I think that you are confusing two things. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. unam. Just a good MD toy ! Victor owner-namd-l_at_ks. edu]Reply All Saturday,. 7b1 - effects of configuration parameters and hardware. washington. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. edu) Date: Wed Sep 29 2010 - 16:34:24 CDT Next message: Gianluca Interlandi: "Re: Re: Experience with Asus Netbook" Previous message: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" In reply to: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" Next in. Entertainment. In the text > field you can enter your atom selection, e. 7 with the PLUMED patch" Messages sorted by: [ attachment ] Hi Gianluca, My guess is that something went wrong while patching namd with plumed. Re: Help building a desktop for namd. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. washington. washington. edu on behalf of Gianluca Interlandi [gianluca_at_u. On Wed, Sep 23, 2015 at 02:28:07PM -0700, Gianluca Interlandi wrote: > The other question in the decision SSD vs HDD is the price tag. >From: Gianluca Interlandi (gianluca_at_u. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you canThe bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. 7 out the door on Friday. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. Re: NAMD 2. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. Choose File -> Save Coordinates. edu> wrote: > What are your simulation parameters: >> >> timestep (and also any multistepping values) >> > 2 fs, SHAKE, no multistepping > > > cutoff (and also the pairlist and PME grid spacing) >> > 8-10-12 PME grid spacing ~ 1 A > > Interlandi G. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. edu> wrote: > Dear all, > > Does anybody have experience simulating carbohydrates with NAMD? In > particular, I'm interested whether the CHARMM or the AMBER force field is > more accurate to simulate carbohydrates. The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. Whitfield, 2 Esther Bullitt, 4 Ronald E. >> >> According to your banchmarks, it looks like the less expensive GTX285 >> (around 300$) performs better than a Tesla C1060 which is 4 times more >> expensive. washington. edu on behalf of Gianluca Interlandi [gianluca_at_u. But, using the PBC my protein is continuous. I was getting 2. I > > attach a plot of a constant velocity simulation where I'm pulling twoRe: NAMD 2. I doubt that there is a way to have NAMD output theFrom: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. Gianluca Interlandi 1 , Minhua Ling, An Yue Tu, Dominic W Chung, Wendy E Thomas Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, United States of America. From: Gianluca Interlandi (gianluca_at_u. uiuc. From: Gianluca Interlandi (gianluca_at_u. uiuc. washington. 100% refund of amount payable if you cancel at least 14 days before check-in. 26588. I wonder whether anybody > has had the same problem and found a solution. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. washington. washington. washington. washington. washington. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. From: Gianluca Interlandi (gianluca_at_u. washington. From: Gianluca Interlandi (gianluca_at_u. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. E-mail: [email protected] > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. From: Gianluca Interlandi [gianluca_at_u. You should simulate it in explicit water (or try one of the implicitGianluca Interlandi is on Facebook. But not now. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. The simulations were not performed at constant velocity > but at constant force. 7 with the PLUMED patch. Biochemistry. edu> wrote: > Hi Fatemeh, > > Thanks for replying. washington. edu) Date: Tue Nov 01 2011 - 14:14:51 CDT Next message: Gianluca Interlandi: "Re: rlwrap problem on" Previous message: Joshua A. You should simulateCorresponding Author. washington. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. Thomas, 2 , * and Evgeni V. Re: external force. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. , the force on the SMD atom gets huge. From: Gianluca Interlandi (gianluca_at_u. com) Date: Sat Jul 04 2015 - 10:49:22 CDT Next message: Gianluca Interlandi: "multicore vs ibverbs" Previous message: Josh Vermaas: "Re: extra bonds" Maybe in reply to: Mitchell Gleed: "Re: replica exchange and GPU acceleration" Next in. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. On the other hand, a 4 TB WD 7200RPM is under 200$. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino: "Re: NAMD 2. edu> wrote:Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. Contact host. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Join Facebook to connect with Gianluca Interlandi and others you may know. washington. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. I would be > happy if somebody could point me out to some scripts which help me performRe: checkpoint software for NAMD? From: Gianluca Interlandi (gianluca_at_u. Reply: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] Dear NAMD users, A portion of my protein is outside of the simulation box. by G. That file contains information how to run >> NAMD (and also compile it. One of the. uiuc. I would be > happy if somebody could point me out to some scripts which help me performOn Fri, Jun 27, 2008 at 9:16 PM, Gianluca Interlandi <gianluca_at_u. >> >> i am attaching some graphs with performance numbers from. washington. washington. washington. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD.