[gmx-users] position restraints

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Mar 25 20:42:58 CET 2013


Ohhh...! :-)
I could not get it on my own independently!
Thanks for all your explanation! Many many thanks.


 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Tuesday, March 26, 2013 12:02 AM
Subject: Re: [gmx-users] position restraints



On 3/25/13 3:25 PM, Shima Arasteh wrote:
> Dear Justin,
> 
> As I got, I need to edit the lipid_posre.itp file. To do so, I need to change numbering of position restraining in lipid_posre.itp file to what they are in their original itp file: In my case popc.itp file.
> Am I right?
> 

More or less, but for the sake of clarity, let me explain this fully so you can hopefully arrive at a resolution quickly.  Say I have a system of arbitrary molecules that have 4 atoms each.  Position restraints only work per [moleculetype], so using genrestr is somewhat dangerous unless you are working with a coordinate file or suitable index file that only specifies a single molecule.  Otherwise, the selection is rather ham-handed and actually gives you a nonfunctional .itp file (hence the WARNING in the help description). Therefore, I can only use atom numbers 1, 2, 3, and 4 in my [position_restraints] directive.  Anything above 4 (i.e. based on selecting multiple molecules in genrestr) triggers a fatal error.

What then happens is that grompp reads those atoms, and every time it encounters those atom numbers within the [moleculetype] (irrespective of how many times that molecule appears), restraints are applied as specified.

So, if you want to restrain only P atoms of every POPC molecule, you basically need a one-line .itp file.  If, for instance, P is atom number 8:

[ position_restraints ]
   8   1   0    0    1000

That will restrain all P atoms (every time they occur, as grompp finds them throughout the coordinate file) in the z-dimension only.  Hopefully that all makes sense and this experience has been educational as far as how these things work.

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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