Durba Roy wrote:
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..
There's not a whole lot more (in terms of specifics) that I can offer. What
might be of use is note 2 here:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints#Notes
There could be some instability in these linear species. I've seen that
reported before. Otherwise, there still could be something wrong with your
tabulated potential (based on your previous post), but you haven't provided any
of that information. I'm sorry to say I have no experience at all with
tabulated potentials, but perhaps someone else can help you out there.
-Justin
Thanks,
Durba
Date: Tue, 11 May 2010 18:37:41 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] energy_increase_NVE_run
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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