[gmx-users] Are water molecules restrained "by default"?

Justin Lemkul jalemkul at vt.edu
Mon Jul 27 23:25:45 CEST 2015

On 7/27/15 5:18 PM, Dawid das wrote:
> Dear Gromacs Experts,
> I read in Gromacs documentation that
> will be interpreted to restrain position of all water oxygen atoms. However
> if I understand it correctly I should define where proper *itp file is
> present as it is for restraining heavy atoms of my protein molecule:
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> I neither use #include mechanism for water oxygens nor #define.
> However I do not get any errors as the documentation suggest when
> POSRES_WATER is not defined.
> So my question is whether using this what grompp has generated regarding
> restraining water oxygens:
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
> is enough to actually restrain those atoms? Or my atoms are not restrained
> after all?
> However if they are, how does Gromacs know what atoms are water oxygen
> atoms? Simply it "recognizes" them because POSRES_WATER flag is used and
> somewhere in my *top file I include *itp file for water molecues:
> #include "charmm27.ff/tip3p.itp"
> ?

Whether or not restraints are applied is dependent upon what you use in the .mdp 
file with the "define" keyword.  See the manual and basic tutorials.



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


More information about the gromacs.org_gmx-users mailing list