[gmx-users] -inf potential with TPIC

[Rafael I. Silverman y de la Vega]

wait, I only changed  the cofactor to gromacs charmm27.ff format


On Tue, Jun 10, 2014 at 1:58 PM, Rafael I. Silverman y de la Vega <
rsilverm at ucsc.edu> wrote:

> 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
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>
>