[gmx-users] -inf potential with TPIC

Justin Lemkul jalemkul at vt.edu
Thu Jun 12 11:47:14 CEST 2014 


On 6/11/14, 8:55 PM, Rafael I. Silverman y de la Vega wrote:
> I mistyped amber, when I should have typed charmm, amber is totally
> uninvolved in  my calculations. I used the script from
> http://www.gromacs.org/Downloads/User_contributions/Other_software titled
> charmm2gromacs. The output looked fine after running it.
>
> And, I doubt its the cofactor,  just ran the insertion with double
> precision mdrun, it gave reasonable looking results. There seems to be some
> sort of issue with unreasonable interaction energies not being discarded
> properly.
>

It's entirely possible that there's something wrong with the tpic code; you can 
certainly file a bug report on Redmine with input files to reproduce it.

-Justin

>
> On Tue, Jun 10, 2014 at 3:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/10/14, 6:14 PM, Rafael I. Silverman y de la Vega wrote:
>>
>>> 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.
>>>
>>>
>> What script did you use?  I don't understand why Amber99SB is involved
>> here, so I don't know exactly what you were doing to create the topology.
>>   It may not end up being useful information, but it's important to
>> establish the validity of the underlying physical model.
>>
>>
>> -Justin
>>
>>
>>> 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
>>>>>>>>>
>>>>>>>>> ==================================================
>>>>>>>>> --
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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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>>>>>> * Please search the archive at http://www.gromacs.org/
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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
>>
>> ==================================================
>> --
>> 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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