[gmx-users] using old energies

Hi everyone, I am simulating proteins in water at the equilibrium. I try to run new simulations with a short protein (deleting atoms from the previous .gro file). I understood that gromacs stores the atom velocities in the .gro file but also in the .edr file! I would like to use the atom veloci

Re: [gmx-users] on NVE and pressure

. Shouldn't the energy be constant in NVE? thanks for helping, loris Berk Hess wrote: From: lorix <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] on NVE and pressure Date: Mon, 16 Apr 2007 12:

Re: [gmx-users] on NVE and pressure

second system had -445679 kJ mol^-1 as average for the 14-114 psec NPT equilibration and -465630 kJ mol^-1 as average for the 300-600 ps of NVE equilibration. greetings loris... Berk Hess wrote: From: lorix <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Disc

[gmx-users] on NVE and pressure

Hi everybody, I am simulating a protein (approximately 5000 atoms) in water (35000 atoms). The protein is out of a thermodynamic equilibrium because I modified a crystallographic structure of one of its conformation (which showed stability with MD). Thus, my aim would be to let the system evo

Re: [gmx-users] parinello-rahman coupling

different trajectories. In my simulations Berendsen barostat can keep the mean value of the pressure, but according to the manual it does not yield a correct thermodynamic ensemble. thanx loris... Tsjerk Wassenaar wrote: Hi Lorix, Sorry for that. You used the word "maintained" fr

Re: [gmx-users] parinello-rahman coupling

. I checked the archives and I did not find much about the mean value. best regards, lorix... Tsjerk Wassenaar wrote: Hi Loris, Enjoying the nice weather here, I'll just give a gentle reiteration of previous remarks. What you observe is caused by the fact that you only have a very small s

[gmx-users] parinello-rahman coupling

Dear gmx-users, I am a new one... coming to the point...I am simulating in parallel different configurations and settings of a protein around 300 residues large plus approximately 12000 water molecules. I am simulating NPT with berendsen for P and T to equilibrate over 100 ps and then the simu