[gmx-users] energy_increase_NVE_run

[Durba Roy]

Hi Justin,

Thank you so much for your reply. Please find attached some of the input 
files for the dye molecule. The table file contains the user defined 
dihedral potential and the negative of its first derivative from -180 to 
180 degrees. The "k" multiplier of the spline is 1 in this case. Looking 
forward to your suggestions..

Thanks,
Durba



Date: Tue, 11 May 2010 18:37:41 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] energy_increase_NVE_run
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4BE9DC35.9060705 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Durba Roy wrote:

> > Hi Gromacs Users,
> > > I am trying to run a NVE simulation of a single dye molecule 
> jumping > from state S0 to state S1. I have starting coordinates and 
> velocities > from a previous NPT run of the same system at S0, 
> however, the charges > are new, that of S1. I didnot generate any 
> Maxwell-velocity for the NVE > run and followed the instructions that 
> rlist should be ~0.3 nm larger > than rcoulomb and rvdw.  I also 
> increased Lincs_iteration value and the > table extension.  Please 
> note that I am using a tabulated interaction > potential for a 
> particular dihedral.
> >   

Simulating under a different ensemble, then changing simulation 
parameters (like cutoffs) does not bode well for simulation stability.  
Note, too, that there are other factors that can influence the stability 
of an NVE run:

http://www.gromacs.org/Documentation/Terminology/NVE

> > The problem is, an increasing total energy during the NVE run and 
> the > molecule collapses followed by segmentation fault. However, the 
> S0-S1 > jump sim runs fine in NPT ensemble.
> > > Also, when I use null potential for the dihedral the NVE job runs 
> fine.
> > Kind of confused and will really appreciate your help.
> >   

If your system is stable without the tabulated potential, then breaks 
down when you use it, it seems pretty clear that however you're treating 
this dihedral is causing your simulation to break.  Without more 
specific details (your full .mdp file, the parameters you're using for 
the dihedral, etc), it will be hard to give you any further help.

-Justin


 > Thanks,
 > Durba
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: topol.top
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100512/5cc73e54/attachment.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: grompp1.mdp
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100512/5cc73e54/attachment-0001.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: out1.gro
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100512/5cc73e54/attachment-0002.ksh>