[gmx-users] using charmm36 force field with gromacs

Thu Nov 5 16:30:46 CET 2015

On 11/5/15 5:33 AM, Catarina A. Carvalheda dos Santos wrote:
> Thank you very much!
>
> Is it possible to add this information about the proper use of constraints
> in CHARMM somewhere?
>

Sure, I'll add it.

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

This is a consequence of the previously mentioned cleanup.  All file format 
information is now hosted at 
http://manual.gromacs.org/documentation/5.1/user-guide/file-formats.html

The new user guide will be much cleaner, informative, and better organized. 
There will be some growing pains as the transition is completed.  Google still 
works for finding the information you need.

-Justin

> 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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>>>>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>
>> ==================================================
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>> Gromacs Users mailing list
>>
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>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
>
>

-- 
==================================================

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

==================================================