jayant james wrote:
To the GMX developers.
Hi!
I am attempting to perform distance restrained energy minimization and I
have a specific doubt regarding the "define" parameter in em.mdp.
To specify distance restraints I include disre= simple in the em.mdp file.
Do I need to specify some thing like "define = -DDISRES"?
Only if you've set up your distance restraints section bracketed by an
#ifdef DISRES ... #endif pair... see
http://wiki.gromacs.org/index.php/include_file_mechanism
I have not seen some thing like this in the gromacs manual but I was
going thro the GMX discussion list and seen some folks define distance
restraints as "define = -DDISRES". I am under the impression that by
specifying disre=simple I automatically turn on distance restraints.
... but only if they're defined. See manual section 4.3.4
Also I saw one person had "gen_vel=yes" in em.mdp is this option possible .
Of course, but it's irrelevant for EM. If you haven't yet worked out
what gen_vel does, then I suspect you need to do some more tutorial
material and/or background reading before you worry about distance
restraints, etc.
Mark
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