[gmx-users] Side chain minimization

Nuno Ricardo Loureiro Ferreira nunolf at ci.uc.pt
Fri Apr 9 15:35:02 CEST 2004

Gaurav Porwal <gauravp at che.iitb.ac.in> escreveu:

> Dear GMX users,
> I need to minimize the energy of a PDB file using the steepest descent
> method. The constraint is that I need to keep the backbone strictly fixed
> with no angle/bond length changes during the minimization and so only the
> side chains should be changing positions to get the minimum energy
> structure.
> Can anybody plz. enlighten how to go about it.
> Thanks in advance.
> Regards,
> Gaurav

Create an index file with the atoms you want to be frozen during EM. You can
use the freeze concept or the restraints concept.

Edit your topology file and mdp file accordingly.


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