[gmx-users] Restrained Molecule is Moving

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 3 03:01:42 CET 2010

Jennifer Casey wrote:
> Hello,
> I am trying to restrain Na+ to a specific position (0.487, 1.620, 1.620) 
> of my box of dimensions 3.2418 X 3.2418 X 3.2418 nm.  The box is also 
> full of 253 THF molecules.  I added the following to the bottom of my 
> .itp file:
> #ifdef POSRES
> #include "posre_Na+.itp"
> #endif
> I wrote the posre_Na+.itp file myself, it just includes the position 
> restraints for Na+, which is atom 1 in my .gro file, and my 
> posre_Na+.itp file deals with atom 1.  The force constants are all 1000.

It does not matter so much whether the atom number is the same, but rather if 
the position restraint definition directly follows the [moleculetype] definition 
of Na+ in your system.  Without seeing your topology file, there's no way to 
know if you've placed the position restraint file in the right place.


> Under the .mdp file, I also made sure that define = -DPOSRES.
> I get no errors when things run, but I do get my Na+ moving around.  
> After I do energy minimization, Na+ ends up at the position (0.373, 
> 1.504, 1.226).  I also do not notice anything about position restraints 
> appearing in my .log file afterwards.
> I really appreciate the help.
> Thank you,
> Jenny


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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