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

[Berk Hess]

Hi,

I quickly ran the tpr file you provided on bugzilla, but I don't see an enormous energy drift.
What do you mean with "the energy explodes"?

Berk

Date: Wed, 21 Apr 2010 11:18:53 -0400
Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve 	simiulations
From: jampanis at gmail.com
To: gmx-users at gromacs.org

Dear Berk,
I am sorry for poor communication, Herewith i am giving my md.mdp file. I this file as you could see i am using two temp coupling groups Tmp1 is protein and a 2nm spherical layer of water around it, and the second one Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K to it. As you could see that from the file below i have taken Tcoupl          = V-rescale and two coupling groups Tmp1 and Tmp2 to make a frozen wall. I am not accelerating any group here.

In other words the goal of simulation is to check the behavior of protein is a confined sphere, i am trying to make frozen wall by freezing water around the protein after a specified distance. 


++++++++++++++++++++++++++++++++++++title           = SS2130cpp             = /usr/bin/cppconstraints     = all-bondsintegrator      = md
dt              = 0.002 ; ps !nsteps          = 1000000 nstxout         = 1000nstvout         = 1000nstfout         = 0nstlog          = 0nstenergy       = 1000
nstlist         = 5ns_type         = gridrlist           = 1.0coulombtype     = PMErcoulomb        = 1.0rvdw            = 1.0rvdw_switch     = 0.9
fourierspacing  = 0.12fourier_nx      = 0fourier_ny      = 0fourier_nz      = 0pme_order       = 4ewald_rtol      = 1e-5optimize_fft    = yes
Tcoupl          = V-rescaletau_t           = 0.1      0.1tc-grps         = Tmp1     Tmp2ref_t           = 283.0    0.0gen_vel         = yesgen_temp        = 283.0
gen_seed        = 181726freezegrps      = Tmp2freezedim       = Y Y Y++++++++++++++++++++++++++++++++++++

Thanks very muchSrinivas.

On Wed, Apr 21, 2010 at 10:53 AM, Berk Hess <gmx3 at hotmail.com> wrote:






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: 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.

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.

--

gmx-users mailing list    gmx-users at 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-request at gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
*********************************************

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: Simplify what you do everyday. Find the right PC for you.
http://windows.microsoft.com/shop
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100422/397429c9/attachment.html>