[gmx-users] -inf potential with TPIC

Wed Jun 11 00:14:53 CEST 2014

I meant that I only changed to cofactor to gromacs chamm27 format, not
amber format. I used charmm27 for the apoprotein as well as the cofactor.

On Tue, Jun 10, 2014 at 3:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/10/14, 6:04 PM, Rafael I. Silverman y de la Vega wrote:
>
>> you think it was the cofactor model?
>>
>>
> If you're using a CHARMM-parametrized cofactor with an Amber99SB protein,
> I'd say the simulations are wholly unreliable.  It's certainly the #1
> likely cause for nonsensical results.  If you want to get to the root of
> the issue, you need to start with a solid foundation.
>
> Unless that's not what your last message meant?  When you say "only
> changed the cofactor," that implied to me that you didn't consistently
> convert everything in the system.
>
>
> -Justin
>
>
>> 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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
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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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
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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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> Gromacs Users mailing list
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