[gmx-users] how to let gromacs NOT calculate intra-molecular electrostatics in a molecule
jalemkul at vt.edu
Wed Oct 21 13:27:04 CEST 2015
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.
> 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
>> 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
>>>> molecule. How to do that?
>>>> Thank you so~ much.
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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