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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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