[gmx-users] Umbrella Sampling settings

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Jul 11 23:10:42 CEST 2013

Thanks for your reply.

But when I don't understand why these extra lines are needed to set when are not advantageous practically! :-(


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, July 12, 2013 1:37 AM
Subject: Re: [gmx-users] Umbrella Sampling settings

On 7/11/13 4:21 PM, Shima Arasteh wrote:
> Hi,
> I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window.
> Some mdp file settings for running US, as I found in US tutorial are :
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance
> pull_dim        = N N Y
> pull_start      = yes
> pull_ngroups    = 1
> pull_group0     = Chain_B
> pull_group1     = Chain_A
> pull_init1      = 0
> pull_rate1      = 0.0
> pull_k1         = 4000      ; kJ mol^-1 nm^-2
> pull_nstxout    = 1000      ; every 2 ps
> pull_nstfout    = 1000      ; every 2 ps
> But I'd like to know which lines are specifically for US? Because in this step, no group is supposed to be pulled but there are some lines written here related to pulling!

All of them are related to umbrella sampling.  Pulling (steered MD) and umbrella 
sampling simply use common parts of the "pull code" in Gromacs because US 
requires a restraint potential.  Whether or not that restraint potential induces 
net displacement (steering, i.e. non-zero pull_rate) or not (zero pull rate, 
restrain to a given set of conditions) is the only difference.  Both processes 
require reference and "pull" groups, geometry information, etc.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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