[gmx-users] -inf potential with TPIC

[Rafael I. Silverman y de la Vega]

you think it was the cofactor model?


On Tue, Jun 10, 2014 at 2:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/10/14, 5:01 PM, Rafael I. Silverman y de la Vega wrote:
>
>> wait, I only changed  the cofactor to gromacs charmm27.ff format
>>
>>
> Pretty amazing that the simulation even ran with that mash-up of
> parameters :)
>
> I'd say that's the most likely cause of your problems; nonsensical
> physical model leads to nonsensical output.
>
> -Justin
>
>
>
>> 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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>>>
>>>
> --
> ==================================================
>
> 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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