Hi,
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.
Berk
Date: Wed, 21 Apr 2010 10:41:25 -0400
Subject: Fwd: [Bug 404] energy increase in nvt and nve simiulations
From: jampa...@gmail.com
To: g...@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.
1.
I have removed the "acc_grps" option
2.
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
system.
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
Srinivas.
--
*********************************************
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
Web:http://jsrao.web.officelive.com/default.aspx
**********************************************
_________________________________________________________________
New Windows 7: Find the right PC for you. Learn more.
http://windows.microsoft.com/shop--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
