[gmx-users] Restrained Molecule is Moving

[Justin A. Lemkul]

Jennifer Casey wrote:
> Thank you so much for your quick response.
> 
> I have attached my .itp, and .top files.  I think that the if statement 
> was originally in the wrong spot, but after changing in and running an 
> energy minimization, there is still some drifting - the Na+ moves to 
> (0.566, 1.559, 1.586) from (0.486, 1.621, 1.621).  Maybe this is normal 
> amount of drift?
> 

Possibly.  Position restraints only specify a force constant to oppose motion, 
not completely fix coordinates, so some movement is possible.  To test, you 
could specify an extremely high force constant (100000 or more) in the posre.itp 
file and see if the position changes any less.

-Justin

> Thanks again,
> Jenny
> 
> On Tue, Feb 2, 2010 at 6:01 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

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