[gmx-users] position restraints

[Shima Arasteh]

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? 


 
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: Monday, March 25, 2013 11:34 PM
Subject: Re: [gmx-users] position restraints



On 3/25/13 3:00 PM, Shima Arasteh wrote:
> Yes, you are right. Because I have read the include mechanism in website many times, but I dont undrestand it in deep! :-(
> I may need to study more.

I would again suggest focusing more on the position restraints contents themselves.  Your formulation for #including them is correct.  The contents of lipid_posre.itp are not.  There is substantial discussion on the topic of position restraints in the manual, as well as the help description of genrestr (especially the part that starts with "WARNING"), which I am willing to bet will solve your issues if you read it carefully.

-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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