[gmx-users] How to write pull code in umbrella sampling
jalemkul at vt.edu
Sat Apr 8 03:07:03 CEST 2017
On 4/7/17 8:56 PM, Qing Lv wrote:
> Dear Colleagues,
> I am trying to do an umbrella sampling using a series of conformations extracted from several unbiased MD trajectories. But I am not sure about the pull code in .mdp file.
> Below is the pull code from the tutorial of Dr. Justin Lemkul :
> define = -DPOSRES_B ; (Why ??)
Did you read the paper I linked from the tutorial, which explains why this is
done for this very specific case?
> ; Pull code
> 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 = 0.0
> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
> Conformations in Justin's tutorial are from steered MD. However, my conformations are not from SMD, and I have not done SMD on this system. So, how to define pull_group1 and pull_group2? And pull_coord1_geometry still set to "distance" ?
The pull groups don't depend on where the configurations came from. They define
the reaction coordinate. You can use whatever pull geometry makes sense; in the
tutorial it is a simple linear reaction coordinate directly along the z-axis.
Other applications may require different definitions.
> Also, need I fix any part of protein in umbrella sampling (with " -DPOSRES ") ? Why?
Generally, no, but you haven't given any useful detail about what your
simulation system is.
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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