[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule

[Justin Lemkul]

On 10/21/15 12:28 AM, li he wrote:
> Thank you for your suggestion, but I just want to skip intra-molecular
> electrostatics, not inter-molecular electrostatics.
> Will set a larger n_rexclude number in the itp file help?
>

nrexcl will exclude *all* intramolecular interactions, including LJ.  AFAIK, 
there is no way to selectively turn off intramolecular charges without turning 
off all intramolecular interactions.  Perhaps you can use tabulated 
interactions, but this may become prohibitively slow.  Why does your physical 
model require no intramolecular electrostatics for running dynamics?  That 
sounds fundamentally unsound to me.

-Justin

> 2015-10-21 9:37 GMT+08:00 Victor Rosas Garcia <rosas.victor at gmail.com>:
>
>> I guess you could try setting all your charges to zero in the topology.
>> Whether the result tells you something physically meaningful is up to you.
>>
>> Just my two cents
>>
>> Victor
>>
>> 2015-10-20 19:46 GMT-05:00 li he <parachuternewyork at gmail.com>:
>>
>>> in other words, I want to just assume ALL intra-molecular electrostatics
>>> (charge-charge interaction) in this
>>> molecule are 0, instead of calculate them in the simulation.
>>>
>>> 2015-10-21 8:43 GMT+08:00 li he <parachuternewyork at gmail.com>:
>>>
>>>> Dear gmxers,
>>>> I am simulating a molecule or about 100 atoms.
>>>> I doNOT want gromacs calculate ALL intra-molecular electrostatics in
>> this
>>>> molecule. How to do that?
>>>> Thank you so~ much.
>>>> yours
>>>> bob
>>>>
>>> --
>>> 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
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> 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
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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