[gmx-users] Restrained Molecule is Moving

[Justin A. Lemkul]

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.

-Justin

> 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
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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