[gmx-users] Constraints in the villin system

[Justin Lemkul]

On 6/1/15 11:55 AM, Mario Fernández Pendás wrote:
> Dear all,
>
> I am interested in simulations with the villin system using the constraint
> algorithm SHAKE.
>  From the physical point of view, does it make any sense to perform a
> simulation only with the hydrogen atoms constrained?
>

Bonds involving hydrogen, not the atoms themselves, yes.  That's fairly standard 
procedure for most simulations.

> Otherwise, when I try to constraint all the atoms using PBC and domain
> decomposition, the LINCS algorithm is suggested and I am still interested
> in using SHAKE.
>

You can certainly try it, but SHAKE is not as stable as LINCS and has problems 
satisfying that many simultaneous constraints.

-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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