[gmx-users] using charmm36 force field with gromacs

Thu Nov 5 18:10:16 CET 2015

Thank you Justin.

On 5 November 2015 at 15:30, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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>>> 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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> 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