[gmx-users] constrained minimization
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:
>[ dihedral_restraints ]
>; i j k l type label phi dphi kfac power
>1410 1393 1391 2610 1 0 -140 0 fc_dihed 2
>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"
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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