[gmx-users] Reference file for harmonic restraints

[Justin Lemkul]

On 7/22/16 9:53 AM, CROUZY Serge 119222 wrote:
> Hi all,
>
> I'm running several sequential minimizations and MD simulations with gromacs after translation of part of my system (the rest being harmonically restrained) and I'm looking for a way to specify unique reference coordinates for all simulations
> The way I understand Gromacs, you define a posres.itp file called by a #define in the .mdp  but the system coordinates used for the restraints are always those read at the start of the run. This is not what I want.. I need to read coordinates to be used as reference (like the REF array in CHARMM) and run all my subsequent simulations
> setting harmonic restraints to these reference coordinates...  Is there an easy way to do this ?
>

Coordinates supplied to grompp -r are used as reference.  If not supplied, the 
default is to fall back to the coordinates in grompp -c.

-Justin

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

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

==================================================