[gmx-users] Restrained Molecule is Moving
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 3 03:30:08 CET 2010
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.
> Thanks again,
> 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:
> 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"
> 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,
> 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
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users