[gmx-users] confusion on NPT MD simulation

[Justin Lemkul]

On 6/16/15 5:27 AM, Ming Tang wrote:
> Dear Justin,
>
> I read a paper, in which the author equilibrated the collagen like this:
> Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in
> which velocity rescaling algorithm with 1ps coupling constant was used. Rigid
> bonds were used to constraint covalent bond length, allowing a time step of
> 2fs. Secondly, a 200ps NPT ensemble with 1bar pressure was used to
> equilibrate the system while keeping the temperature at 310 K, where
> Berendsen barostat with 1ps coupling constant was adopted. In this step, the
> whole protein was held fixed. Lastly, we further equilibrated the system in a
> NPT ensemble for 400ps, with a more accurate pressure coupling algorithm
> based on Parrinello-Rahman barostat (Parrinello and Rahman 1981). Only the
> first and the last C − α atoms of each chain were constrained.
>
> I wonder whether they used genrestr to restrain atoms, like utilising -fc to
> add a quite large force in all directions to them, and considered those atoms
> are kept fixed during NPT equilibration?
>

People are often lazy (or inconsistent) with language.  Holding something 
"fixed" might mean "huge restraint" or it might actually mean frozen (freezegrps 
in the .mdp).  There are functional differences between these two.  Atoms are 
also not "constrained" (that's a restraint!) in GROMACS, so there may be some 
loose language here...

If you have questions about methods for published work relevant to what you're 
doing, that's what corresponding authors are for!

-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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