[gmx-users] position restrain energy

[Justin Lemkul]

On 4/19/16 9:57 AM, Nikhil Maroli wrote:
> reference previous mail thread :
> https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg18799.html
>
> Dear Justin,
> Thanks ,so i have to define restrain for individual molecules.in that case
> how should i define *mdp file ,since eight restrains are there for each
> ring A,B,C,D,E,F,G,H .
> in mpd define      = -DPOSRES   what name i will give here,
>

If you have multiple #ifdef keywords, you need a series of define statements, e.g.

define = -DPOSRES_PROTA -DPOSRES_PROTB...

If the restraints are all meant to be on at the same time, then just put each 
restraint file within an #ifdef POSRES ... #endif block.  Having separate 
keywords is only necessary if you need some restraints on while others are off.

-Justin

>
> topology looks like
>
> #include "toppar/PROA.itp"
> #ifdef POSRES_PROTA
> #include "posre_cpn.itp"
> #endif
>
> #include "toppar/PROB.itp"
> #ifdef POSRES_PROTB
> #include "posre_cpn.itp"
> #endif
> #include "toppar/PROC.itp"
> #ifdef POSRES_PROTC
> #include "posre_cpn.itp"
> #endif
> #include "toppar/PROD.itp"
> #ifdef POSRES_PROTD
> #include "posre_cpn.itp"
> #endif
> #include "toppar/PROE.itp"
> #ifdef POSRES_PROTE
> #include "posre_cpn.itp"
> #endif
> #include "toppar/PROF.itp"
> #ifdef POSRES_PROTF
> #include "posre_cpn.itp"
> #endif
> #include "toppar/PROG.itp"
> #ifdef POSRES_PROTG
> #include "posre_cpn.itp"
> #endif
>
>
> #include "toppar/PROH.itp"
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================