[gmx-users] RE: About Potential energy calculation

Hi, Won Ok, what I did was not exactly as is described. I attach the bash script that I made to do this I use the trajectory file to extract EACH frame and safe it in an independent file using trjconv . And when I do the extraction, I only extract the protein of interest, this can be done bec

[gmx-users] Re: pdb2gmx

Hi Valentina The first lines of your rtp files should be something like this where you specify the type (function) of the interaction [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 5 921 3 1 0

[gmx-users] About low PH simulation of DPPC liposomes

Hi guys I need to simulate DPPC liposomes in low PH environment I have been looking for literature but I have not found a good option. Any suggestion?? Thanks John Michael -- View this message in context: http://gromacs.5086.x6.nabble.com/About-low-PH-simulation-of-DPPC-liposomes-tp5008759

[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?

Hi guys I am using the set of parameters that I added before and I am getting energy Conservation THANKS John -- View this message in context: http://gromacs.5086.x6.nabble.com/Have-your-ever-got-a-real-NVE-simulation-good-energy-conservation-in-gromacs-tp5008501p5008756.html Sent from the

[gmx-users] grommp problem in gromacs 4.6.1

Hi guys I am trying to generate a .tpr file using grommp in gromacs 4.6.1. Unfortunately I am obtaining a very strange error: --- Program grompp, VERSION 4.6.1 Source code file: /N/u/ortgrp/Quarry/src/gromacs-4.6.1/src/kernel/toppush.c, line: 133

[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?

Hi Guys Thanks for your reply 1. Ok guys I will use the following Double precision gromacs dt=1fs pbc = xyz nstlist = 5 rlist= 1.7 rlist_long = 2.0 coulombtype = PME-Switch rcoulomb_switch = 1.2 rcoulo

[gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs?

Hi Guys I have been trying by all means to get a real good Energy conservation in NVE simulations using gromacs but it has been almost impossible for me. I have tried many different combinations of Coulomb and VdW parameters and changed the cut off radius and nothing. 1. Have you ever obtained en

[gmx-users] Re: About Potential energy calculation

Hi Justin Thanks for your answer. Actually, you are right and that is what I am doing now, but it is really time consuming and it is like double calculating because the potential energy is computed during the MD. Any way thanks John Michael -- View this message in context: http://grom

[gmx-users] Re: About Temperature coupling and Energy Transfer....

Dear Justin Thanks for your answer. I know what you mean, but the problem is that this is not a possible physical (real) behaviour. If the temperature is not controlled as you said, the energy should continue growing not stop, but in these case after 50ps it reaches some kind of equilibrium a