[gmx-users] On posre.itp
Mr Bernard Ramos
bgrquantum at yahoo.com
Sat May 7 11:16:27 CEST 2011
Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks.
--- On Sat, 5/7/11, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] On posre.itp
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, May 7, 2011, 5:10 PM
On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote:
I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms.
Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC).
Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks.
Up to you. Do you want to sample under unphysical restraints or not?
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