[gmx-users] -inf potential with TPIC

Rafael I. Silverman y de la Vega rsilverm at ucsc.edu
Tue Jun 10 22:58:38 CEST 2014

I suppose something might be wrong with the simulations. I am using gromacs
4.6.5, I am simulating a protein with a cofactor, someone else parametrized
it, I changed from charmm to gromacs amber99sb.ff format with a script on
the gromacs website.  I did a typical em/nvt/npt equilibration  followed by
a 5 ns production run. I picked 250 frames out of the trajectory, and
altered them to the TPIC input format with a script I wrote, to insert the
particle half way between two atoms that I chose. I am inserting a water
molecule. When I run the actual insertion some of the frames have a
reasonable looking mu, and some have -inf mu. I think it may have to do
with cavity size, some frames have too small of a cavity, so the
interaction energy of the inserted water diverges...

On Mon, Jun 9, 2014 at 6:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 6/9/14, 6:41 PM, Rafael I. Silverman y de la Vega wrote:
>> Hi all, I am having a problem with -inf mu coming out of TPIC
>> calculations.
>> Anyone have some suggestions on how to avoid this? Tabulated potentials?
>> Or
>> can I modify the source code to reject the absurd values that cause this?
>> I
>> read a few old discussions on this, I didnt see much on how to handle
>> this.
> I'd be much more concerned that something is going wrong in the
> simulations.  I have no experience with TPIC, but if you post more detailed
> information about what you're doing and which Gromacs version you're using,
> you're more likely to get some suggestions.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
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> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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