[gmx-users] Constant-velocity pulling

[Justin Lemkul]

On 6/8/16 9:51 AM, Sajjad Kavyani wrote:
> Dear experts,
> I'm trying to do a constant-velocity pulling of water particles through a
> tube.
> First, I did the process with a constant force constant successfully but
> now for the constant velocity, I do not get how to choose parameters in the
> .mdp file!.
> I read the umbrella sampling tutorial, manual and actually did a search in
> the mailing list mails but some how I'm nervous to choose between!
>
> This is the the pull code for the constant force pulling:
> ;;; Pull code:
> pull                          = constant-force
> pull-geometry = direction-periodic
> pull-ngroups = 1
> pull_group1_name   = W
> pull-coord1-vec  = 0 0 1
> pull-coord1-k = 50
> pull-coord1-groups = 1
>
> 1. Could you please tell me how to modify the above code for the constant
> velocity (for example v=v0) pulling and explain to me the parameters ?
> 2. And what is exactly the "pull-coord1-groups" parameter and how to choose
> the correct value? If I have tow group to pull (one with constant-force and
> another with constant-veocity  )?
>

My umbrella sampling tutorial goes over all of this in detail.  Take another look.

-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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