[gmx-users] To the GMX developers-distance restraints

[Mark Abraham]

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