[gmx-users] How to write pull code in umbrella sampling

[Justin Lemkul]

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

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

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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