Justin A. Lemkul
jalemkul at vt.edu
Thu May 13 00:52:33 CEST 2010
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:
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.
> 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:
>> > 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
>> > 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.
> > Thanks,
> > Durba
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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