[gmx-users] distance restraints in mdp

[Justin Lemkul]

On 3/7/16 10:35 PM, Sana Saeed wrote:
> i am performing protein ligand binding free energy calculation MD. i have
> applied distance restraint to 1 pair of atoms. now when i am running md it
> gives me LINCS warnings. first i thought it is because of wrong geometry so i
> changed complex, now i am doing it for Lysozyme+JZ4. but still same warning.
> i am confused about the distance restraints to be introduced in mdp file.
> disre = simple/ensemble? i read in manual, but still confused. i tried both
> with "simple it gives me LINCS warning and with ensemble it says that this
> version of gromacs doesnt support it. i am using 5.1 gromacs.

Then simplify further and make sure the system runs without restraints or 
anything else.  Just normal MD.  Start simple to avoid chasing the wrong problem.

-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

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