[gmx-users] The flat-bottomed position restrain in the topolgy file

[Justin Lemkul]

On 10/16/14 8:12 AM, liuyong_1007 at dicp.ac.cn wrote:
> Dear gromacs usres,
>
> The format of the flat-bottomed position restrain in the topolgy file is
> [position_restraints]
> ; num. atoms    func.type   g      r(nm)    k(KJ*mol-1*nm-2)
>      1              2        1       1.0         1.0
> as given in the manual 5.0.2.
> But there is still another parameter not set. The reference position R_i ( see eq. 4.77 in the manal)is not given in the topolgy file.
> How can this parameter be set ?
>

Like all position restraints, the reference coordinates are taken from grompp 
-c, unless -r is specified, in which case the reference coordinates are taken 
from -r.

-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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