Re: [gmx-users] Does shell molecular exclude core shell electrostatics automatically

2009-11-25 Thread David van der Spoel
Shuangxing Dai wrote: Hi, all, I was wondering if the shell molecular dynamics exclude the electrostatic interaction automatically. According to the shell model, the interaction between core and shell in replaced by the harmonic interaction. If not, how to exclude electrostatic in

[gmx-users] Simulation at unrealistic temperatures

2009-11-25 Thread Neha Bharat Gajaria
Dear List, I m trying to run an NPT simulation at 600K which looks unrealistic. I m running minimization followed by anealing and then NPT simulation (mdp files are attached). The job keeps running but after 162 ps, the CPU usage gradually decreases to 26% without any further output. Your help is

[gmx-users] Does shell molecular exclude core shell electrostatics automatically

2009-11-25 Thread Shuangxing Dai
Hi, all, I was wondering if the shell molecular dynamics exclude the electrostatic interaction automatically. According to the shell model, the interaction between core and shell in replaced by the harmonic interaction. If not, how to exclude electrostatic interaction between them?

RE: [gmx-users] Unexpected behavior of g_msd

2009-11-25 Thread Dallas B. Warren
trjconv Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hamme

[gmx-users] Unexpected behavior of g_msd

2009-11-25 Thread Darrell Koskinen
Hi Tsjerk, I looked at the .trr file and cannot read this file and simply delete lines to create a sub-trajectory. So, how do I create a sub-trajectory to analyze? Thanks. Darrell Date: Wed, 25 Nov 2009 09:04:01 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Unexpected behavior of

Re: [gmx-users] Tabulated non-bonded potential

2009-11-25 Thread ms
I have a further question about tabulated non-bonded potentials. The manual (6.7.2) says: "It is also possible to combine a standard Coulomb with a modified LJ potential... The table file must always contain the 7 columns however, and meaningful data (i.e. not zeroes) must be entered in all column

Re: [gmx-users] g_msd => The MSD and periodic boundary condition

2009-11-25 Thread Tsjerk Wassenaar
Hi, > Removing periodicity from the trajectory can be done after simulation > using g_traj with the "-nojump" option. Actually, trjconv -pbc nojump Cheers, Tsjerk > > Best, > Lukasz > > -- > Lukasz Cwiklik > http://cwiklik.wordpress.com > -- > gmx-users mailing list    gmx-us...@gromacs.org >

Re: [gmx-users] hi

2009-11-25 Thread Justin A. Lemkul
Please choose an informative subject line, as it will help attract the attention of someone interested in helping you. PAVAN RELISH DESTINY RESOLVING CRUX OF LIFE. wrote: I am new to Gromacs & using it with Amber force field amber03, i am able 2 run my system

Re: [gmx-users] g_msd => The MSD and periodic boundary condition

2009-11-25 Thread Lukasz Cwiklik
On Tue, Nov 24, 2009 at 1:09 PM, Omer Markovitch wrote: > On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin wrote: >> >> So, how can I remove the periodic boundary condition to get the truly >> movement of the atoms between the two time steps ? > > Removing PBC and placing atoms back into their "true"

[gmx-users] output of mdrun-openmm

2009-11-25 Thread hhei...@terra.es
Dear all, We are experimenting with mdrun-openmm on a high end Nvidia Type graphics card and CUDA attached to the local NGS cluster computer. The simulation for smaller systems runs fine, but when one moves to bigger files it turns out that all the result files (xtc, pdb edr and log) are stored

RE: [gmx-users] query regarding itp file

2009-11-25 Thread Kukol, Andreas
That info is in the GROMACS manual - a very nice manual with lots of effort put in to answer such questions. A. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of subarna thakur [thakur.suba...@yahoo.co.in] Sent: 25 November

[gmx-users] query regarding itp file

2009-11-25 Thread subarna thakur
Hi Can any body please tell me what does c0 and c1 column represent in .itp file? And how do I obtain these parameters for a ligand. Subarna thakur The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] does editconf follow pdb rules?

2009-11-25 Thread Francesco Pietra
Hi: In my hands, the command editconf -f input.gro -o output.gro does not follow the PDB rules as regards the residue name. W from the .gro file (obtained by genconf -f water.gro -nbox 2.5 2.5 2.0 -0 out.2.5.2.5.2.0.gro) where water.gro is from MARTINI web page, is placed correctly as atom (co

Re: [gmx-users] Unexpected behavior of g_msd

2009-11-25 Thread Tsjerk Wassenaar
Hi Darrell, You can check whether the output is identical to a trajectory of the specified frames... It may well be that the counting for the regression is done on the frames read: 100 - 60 = 40 ps Then 4 and 35.9 would correspond to 64 and 95.9. The answer is in the code... But using a subtrajec

[gmx-users] hi

2009-11-25 Thread PAVAN RELISH DESTINY RESOLVING CRUX OF LIFE.........
I am new to Gromacs & using it with Amber force field amber03, i am able 2 run my system of DNA till steepest descent but when i tried to run it for cg it showed that can not work with so much of constrains so i tried to run it with -Dposres dire