[gmx-users] Regarding constraints

[Justin Lemkul]

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

-- 
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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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