[gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Berk Hess gmx3 at hotmail.com
Wed Apr 21 16:53:28 CEST 2010


I moved this to the user list, so it will be of use to others.

I have no clue what you are trying to do, what groups you are accelerating or freezing.
So we can't help you without further information.
Setting up simulations with frozen groups, accelerate groups or different coupling
temperatures is tricky and will in most cases destroy energy conservation.


Date: Wed, 21 Apr 2010 10:41:25 -0400
Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations
From: jampanis at gmail.com
To: gmx3 at hotmail.com

Dear Berk,

Thanks for the reply, based on the suggestions of Justin from 
Mailing list i have tried the simulation in the following way.

 I have removed the "acc_grps" option
 I have used "energygrp_excl" to avoid
 interaction between non frozen-frozen and frozen-frozen.

Still i have seen some velocity to the frozen atoms (i have printed 
velocities from trajectory) and drift in the energy.

3. I also 
switched of PBC and used "coulombtype = different options here"  In this case
 i observed that some of the water molecules try to escape from the 

But i am not clear about center of mass motion. Should i allow 
to change center of mass with "comm_mode = No" option?

Could you please 
let me know if you want more details about this? I am still struggling 
with running this simulation.

Thanks for your kind help

J. Srinivasa Rao 
Post-doctoral Research Associate
C/o Prof. Luis R Cruz Cruz
Computational Biophysics Group

Department of Physics
Drexel University
3141 Chestnut St
Philadelphia, PA 19104, USA.
Ph:  Off:     215-895-1989
        Mob:  704-706-4191


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