[gmx-users] Umbrella Sampling settings

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jul 12 18:03:11 CEST 2013

Yes, I got Thomas response and I am so grateful in this about. :-)

Also many many thanks for your response Justin.

Although I don't know the definition of pull-vec yet and I need to study in this about, Would you  please let me know if the grompp knows what I wrote as the COM of protein or not? And if it recognizes which ion I mean to be pulled among many ions exist in the whole system? How is it?


----- 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 8:16 PM
Subject: Re: [gmx-users] Umbrella Sampling settings

On 7/12/13 11:32 AM, Shima Arasteh wrote:
> Allright.
> As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system.
> An ion is considered in center of the each window, the reaction coordinate is set to z,  so the group which is pulled is an ion, and my ref group would be COM of the protein. But I don't know what statement is supposed to write in mdp settings exactly:
> ; Pull code
> pull            = umbrella
> pull_geometry   = position
> pull_dim        = N N Y
> pull_start      = yes
> pull_ngroups    = 1
> pull_group0     = COM of protein
> pull_group1     = ion
> 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
> IN fact, to implement such settings, how I make the US understand to get the COM of protein as the ref group and the proposed ion as the pulled group?
> Would you please give me any suggestions?

You got a very thorough response already today:


I see that your settings are now different, using "position" geometry instead of 
"distance," which is good because that's a better approach for your system. 
What you haven't specified is pull_vec1, which is necessary when using 
"position" geometry.

All of these details are discussed to some extent in my umbrella sampling 
tutorial; it should certainly serve as a basic guide.  What you're trying to do 
is ultimately going to require a slightly different approach, but the general 
principles and explanations of .mdp terms are the same.



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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