[gmx-users] Position restraining of ions.

Justin Lemkul jalemkul at vt.edu
Thu Jul 16 13:47:20 CEST 2015

On 7/16/15 6:22 AM, Gordan Horvat wrote:
>   #ifdef REST_ON
>   #include "POT_rest.itp"
>   #endif
> should go at the end of POT_rest.itp file and
>   #ifdef REST_ON
>   #include "CL_rest.itp"
>   #endif
> should go at the end of CL.itp file. The restraint you listed restraints the
> first atom of every molecule of the type stated in the corresponding itp file.
> Since potassium and chloride ions are monoatomic, that should work fine.

Neither of the #ifdefs have to be in the actual .itp files.  They must 
correspond to the [moleculetype], and since they are appropriately listed 
consecutively here, this approach works fine.

> Elsewise, you can just put the line
>   #include "ionX_rest.itp"
> at the end of the ionX.itp file which will turn on restraints automatically
> without having to define -DPOSIONX keyword in mdp file.

This is dangerous because then the restraints are *always* on, which is usually 
undesirable.  If you forget to modify the files if conditions change, then run a 
long simulation...



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


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