abdullah ahmed wrote:
Hello,
I would like to restrain my molecule to a specific position in space. I
would like for certain atoms to lie on the y-axis. To do this I used
the following code/lines in my .top file:
[ position restraints ]
This is an incorrect directive. It should be position_restraints.
2 1 1000 0 1000 ;
3 1 1000 0 1000 ;
4 1 1000 0 1000 ;
5 1 1000 0 1000 ;
6 1 1000 0 1000 ;
7 1 1000 0 1000 ;
8 1 1000 0 1000 ;
9 1 1000 0 1000 ;
Unfortunately, after minimization my file contained the molecule in the
same position as when the restraints were not applied.
Does anyone know what I am doing wrong?
Perhaps the directive name is an issue, although I think grompp should have
raised a warning of some sort. Otherwise, is this block within the appropriate
[moleculetype] in the topology? Is it under control of an #ifdef block that you
haven't invoked in the .mdp file?
-Justin
Thanks in advance,
Abdullah
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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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