[gmx-users] Regarding constraints
jalemkul at vt.edu
Fri Sep 30 15:26:43 CEST 2016
On 9/30/16 9:22 AM, Apramita Chand wrote:
> Dear Gromacs Users,
> Can I use LINCS constraints instead of SHAKE algorithm while using
> GROMOS53a6 forcefield? Also, if I want to conduct hydrogen bond property
Sure, LINCS is more stable than SHAKE.
> calculations, what should I set the constraint option to in my .mdp file?
Hydrogen bonding is a noncovalent interaction type and has nothing to do with
intramolecular constraints. If you are interested in, e.g. distributions of
bonds containing H, then you shouldn't be constraining anything (because those
bond lengths are, by definition, constant). But that's not how most modern
force fields are used and it limits the maximum time step significantly.
> I'm having the constraint option as 'h-bond' now. Is it right or should I
> change it to 'all-bond'?
> In the original GROMOS53a6 paper, the simulations were run as "all bond
> lengths constrained using SHAKE algorithm with relative geometric accuracy
> of 10-4s".
This means "constraints = all-bonds"
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
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