[gmx-users] using charmm36 force field with gromacs

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Thu Nov 5 11:33:53 CET 2015


Thank you very much!

Is it possible to add this information about the proper use of constraints
in CHARMM somewhere?

Also, at
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM some
of the links are broken, including the link to the mdp file.

Cheers,

On 4 November 2015 at 13:51, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/4/15 8:50 AM, Mark Abraham wrote:
>
>> Hi,
>>
>> Pages are back at
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields
>>
>>
> Outstanding, thanks Mark.
>
> -Justin
>
>
> Mark
>>
>> On Wed, Nov 4, 2015 at 1:14 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 11/4/15 4:52 AM, Catarina A. Carvalheda dos Santos wrote:
>>>
>>>> Hi Justin,
>>>>
>>>> Regarding the nonbonded settings for protein-membrane simulations using
>>>> CHARMM.
>>>> The information you provided used to be available at http://www.
>>>> <
>>>>
>>>
>>> http://www.google.com/url?q=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FTerminology%2FForce_Fields%2FCHARMM%3Fhighlight%3Dcharmm&sa=D&sntz=1&usg=AFQjCNExpa_o_HvFT4jyZ4M99zVk-TyRwQ
>>>
>>>>
>>>> gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>>>> <
>>>>
>>>
>>> http://www.google.com/url?q=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FTerminology%2FForce_Fields%2FCHARMM%3Fhighlight%3Dcharmm&sa=D&sntz=1&usg=AFQjCNExpa_o_HvFT4jyZ4M99zVk-TyRwQ
>>>
>>>> ,
>>>> but I do not seem to be able to find it now (even using the search
>>>>
>>> engine).
>>>
>>>>
>>>> I know the GROMACS website has gone through some changes lately, so
>>>> maybe
>>>> this was just moved somewhere else.
>>>> Could you please tell us where we can find it now?
>>>>
>>>>
>>> The page was deleted during a recent wiki cleanup/purge.  I hope it will
>>> be
>>> reinstated, along with some of the other useful force field pages that we
>>> had.
>>>
>>> -Justin
>>>
>>> Kind regards,
>>>>
>>>>
>>>> On 4 November 2015 at 08:43, Erik Marklund <erik.marklund at chem.ox.ac.uk
>>>> >
>>>> wrote:
>>>>
>>>>
>>>>> On 3 Nov 2015, at 23:51, Justin Lemkul <jalemkul at vt.edu<mailto:
>>>>> jalemkul at vt.edu>> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On 11/3/15 6:45 PM, Erik Marklund wrote:
>>>>>
>>>>> On 3 Nov 2015, at 23:02, Justin Lemkul <jalemkul at vt.edu<mailto:
>>>>> jalemkul at vt.edu><mailto:jalemkul at vt.edu>> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On 11/3/15 5:53 PM, Erik Marklund wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Use constraints = h-bonds
>>>>>
>>>>> You'll get incorrect balance of 1-4 interactions if you constrain all
>>>>> bonds with CHARMM.
>>>>>
>>>>> Interesting. Can you please elaborate Justin?
>>>>>
>>>>>
>>>>> Think about a simple C-C-C-C dihedral.  In our CHARMM parametrization,
>>>>>
>>>> we
>>>
>>>> assume all of those bonds to be harmonic and tune the dihedral energy
>>>>> surface against QM target data that have only one constraint - the
>>>>>
>>>> dihedral
>>>
>>>> itself.  Therefore, the bond lengths can vary, and since the dihedral
>>>>>
>>>> term
>>>
>>>> and the 1-4 nonbonded terms are interrelated (and everything else is
>>>>> excluded), the balance of forces depends on the correct application of
>>>>>
>>>> the
>>>
>>>> bonded terms.  So to use the force field in the same manner as it was
>>>>> parametrized, constrain only bonds involving H.
>>>>>
>>>>>
>>>>> Thanks. I do get that. But is charmm any different from other widely
>>>>>
>>>> used
>>>
>>>> protein force field in this respect?
>>>>>
>>>>>
>>>>> Not that I'm aware.  Again, given the magnitude of the fluctuations of
>>>>> bonds, the magnitude of any error would probably be extremely small so
>>>>> I
>>>>> would not expect serious problems if one were to constrain all bonds.
>>>>>
>>>> Just
>>>
>>>> pointing this out for the sake of being pedantic, but it is something I
>>>>> think should be done properly, since the functional form assumes it in
>>>>>
>>>> the
>>>
>>>> parametrization.
>>>>>
>>>>> -Justin
>>>>>
>>>>> Right. Thanks for clarifying Justin.
>>>>>
>>>>> Erik
>>>>>
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu<mailto:
>>>>>
>>>> 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 629
>>> 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 629
> 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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> posting!
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>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK


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