[gmx-users] Umbrella Sampling _ pulled ion

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jul 24 17:53:36 CEST 2013

Yes, Thanks.

Would you give me a hint on this fact that how I would be sure that I am running a correct US ? with proper settings?
To save time, I' d prefer to run the US.mdp just for one window. Do you agree with me that if I run an incorrect US for any of the windows, I would get an odd result for npt_US or md_US?

Many many thanks for your time and suggestions.


----- 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: Wednesday, July 24, 2013 8:05 PM
Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion

On 7/24/13 11:30 AM, Shima Arasteh wrote:
> Hi,
> I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane.
> In order to do so, I tried to set a specific ion ( Ces with the atom number 85563) as the pull_group1 in mdp file:
> pull_group1     = Ces_ion
> So I had to get a new group named Ces_ion contains of Ces 85563. Therefore made a new index file ( index_US.ndx). In this ndx file, there is an extra group in addition of existed groups as this( The last 2 lines in ndx file) :
> [ system]
> ...
> [protein]
> ...
> [protein-H]
> ...
> [ Ces_ion ]
> 85563
> But after running the grompp, I get this fatal error:
> File input/output error:
> index_US.ndx
> Would you please let me know how I would be able to define a new group for a specific ion ?
> Did I make a mistake in defining a new group?

What you did in terms of index group content is fine.  The error message means 
that the file called "index_US.ndx" is not present in the working directory, or 
it has the wrong permissions.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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