[gmx-users] Umbrella Sampling _ pulled ion

[Shima Arasteh]

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.

 
Sincerely,
Shima


----- 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>
Cc: 
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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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