[gmx-users] constrained minimization

rob yang nextgame at hotmail.com
Wed Jan 11 06:20:28 CET 2006

>From: David Mobley <dmobley at gmail.com>
>There *is* an option for dihedral restraints in GROMACS if that's what
>you're after (not sure if you are trying to distinguish between
>*constraints* and *restraints*). You can of course minimize with
>dihedrals, distances, and angles *restrained*, but this is a different
>thing from minimizing with *constraints* on those things. Dihedral
>*restraints* are like this:
>topology file:
>[ dihedral_restraints ]
>; i j k l            type     label  phi  dphi  kfac          power
>1410 1393 1391 2610  1        0      -140  0  fc_dihed     2
>mdp file:
>define = -Dfc_dihed=41.84

Thanks David. Yes constraint = restraint in my last message. Where do you 
find the documentation for the [dihedral_restraints], because i didn't find 
it in the manual.
Just so that i understand it correctly, the restraint is of the form:
fc_dihed *(phi-dphi) ^power

so what then is type (1 for proper 2 for improper?!) and what is label?..
and can i define my fc_dihed in my .top file directly? what is the advantage 
of defining it in the .mdp file
what do dihre=simple, and dihre-fc=1 mean? are there any other "keywords" 
out there?

much appreciated if you can give me a pointer or 2 to the above questions. 
Thank you very much in advance.


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