[gmx-users] -inf potential with TPIC

João M. Damas jmdamas at itqb.unl.pt
Thu Jun 12 16:07:26 CEST 2014 

Hello Rafael,

High energies (energy differences) are not discarded. When summing them
through the exponential of their negative, they contribute very little to
the final sum (lower energies dominate the sum). Hence, they are
"discarded".

The "-inf" value on the mu standard error output is normal because, unlike
the -tpi output, there is no ternary operator checking if the sum of
exponentials is equal to zero (when it is, the log of zero gives you the
inf value).

The change to the double precision not giving you the "-inf" also makes
sense, because the sum of exponentials, which on single-precision was zero,
can now be non-zero due to the higher number of decimal places on
double-precision. I am guessing with double-precision you are getting very
high positive numbers (energies) for the mu, around 1000 maybe?

My interpretation is that it is hard to find a "favorable place" to insert
the water molecule in that cavity, at least with a few frames. I am
guessing that with more and more frames, that may change, which is natural.

I hope this has helped.

Cheers,
João



On Thu, Jun 12, 2014 at 10:45 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>>>>>>>
>>>>>>>>>> ==================================================
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>>
>>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>
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>>>>>>>>>> gmx-users
>>>>>>>>>> or
>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>     --
>>>>>>>>>
>>>>>>>>>  ==================================================
>>>>>>>>
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
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>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>>>>
>>>>>> ==================================================
>>>>>
>>>>> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

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