[gmx-users] position restraints

[Shima Arasteh]

Would you please let me know that what subject I need to look for through manual or threads? Making index groups of multiple atoms?


Thanks for your 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: Monday, March 25, 2013 10:22 PM
Subject: Re: [gmx-users] position restraints



On 3/25/13 1:50 PM, Shima Arasteh wrote:
> Yes sir!
>
> What I have in my top file is :
> ; Include forcefield parameters
> #include "./charmm36-modified.ff/forcefield.itp"
>
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef POSRES
> #include "protein_chain_A_posre.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef POSRES
> #include "protein_chain_B_posre.itp"
> #endif
>
> ; Include POPC chain topology
> #include "popc.itp"
> #ifdef POSRES_LIPID
> #include "lipid_posre.itp"
> #endif
>
> ; Include water topology
> #include "./charmm36-modified.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "./charmm36-modified.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> POPC        238
> SOL         18706
> NA               615
> CL               617
>
>
> I used genrestr to create the itp file of P atom types.The generated itp file is lipid_posre.itp. If I need to send any other information please let me know.
>

In that case, lipid_posre.itp should have only one line.  If you've made an 
index group of multiple P atoms across multiple molecules, that is the incorrect 
approach.  Consult the manual, website, and numerous threads in the archive.

-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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