Thank you Justin, I want to do QM calculationbefore running equilibration then
run the MD simulation by GROMACS. Do you knowwhich software is appropriate and
compatible with GROMACS that after QM calculation I can run the rest of
simulation?
Best, Mohammad.
On Thursday, March 31, 2016 3:43 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/30/16 2:17 AM, mohammad r wrote:
> Hi gromacs users,
>
>
>
> I want to do QMcalculation to my system. Can the PRODRG sitedo it (according
> to gromacs tutorial)? Or I should do it by using gromacsitself? By the way
QM calculations are not reliant on MM topologies, like those from PRODRG (which
are poor quality anyway) or any force field terms.
GROMACS does not do QM directly, though there are interfaces to popular QM
codes
for doing QM/MM. For strict QM, abandon GROMACS and use the appropriate
software.
> I’ve generated the initial coordinate and topology files inamber tools then
> convert it to gromacs format by using parmed (because theforce field which I
> want is not included in gromacs).
>
Again, for a pure QM calculation, there is no need for any MM programs or force
fields.
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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