[gmx-users] constraints

[Justin Lemkul]

On 5/12/14, 9:50 AM, Nicola Staffolani wrote:
> OK, got it, thanks a lot Justin! ;) .0005 ps is indeed working...
> It is not clear to me what I miss - from the Chemistry or Physics point of
> view - when I constraint the X-H bonds... I mean, will the "rest of the
> dynamics" (for example, the oscillations of the other couples of bonded
> atoms) be affected if the H-X bonds are constrained, so that my results do
> not make sense any more?
>

Your results certainly make sense.  You'll have to dig a bit deeper into the 
underlying theory, of course, but constraints are routine and widely used. 
There was a great discussion about this just a few weeks ago.

> By the way, in my case where I am getting WARNINGs regarding N-H bonds,
> constraints = h-bonds
> looks to be a convenient way to fix the problem, if I do not want to make
> dt smaller: is that advisable?
>

Yes.  Most simulations are run with at least X-H bonds constrained.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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