[gmx-users] I want to drag two atoms together with GROMCS SMD options.
jalemkul at vt.edu
Thu Mar 9 13:56:16 CET 2017
On 3/9/17 3:00 AM, Vytautas Rakeviius wrote:
> I want to drag two atoms together with GROMCS SMD options.But I tried different options and still those groups are pushed away one from another.I would be very thankful if someone edits this code example (from: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_pull.mdp) in such way that Chan_A and Chain_B comes together into covalent bounding rage or similar:; Pull code
A negative pull rate causes the two groups to approach (e.g. distance
decreases), in contrast to the tutorial settings quoted below in which a
positive pull rate causes a dissociation/distance increase.
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = Chain_B
> pull_group2_name = Chain_A
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
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
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