[gmx-users] SA again

Nuno R. L. Ferreira nunolf at ci.uc.pt
Wed Apr 28 20:54:01 CEST 2004

Hi Osmany

Reading your question again, the interpretation was a bit different.
You were talking about constraints (LINCS,SHAKE,SETTLE) and I was thinking 
about position restraints.

IMHO, I think you should use constraints during your SA run.  If you do not 
use bond contraints for e.g., you have to be carefull with your time step.  
So if you are going to use dt=0.002 use constraints, if not, the bond lenghts 
will be outside "normal" ranges, and in place of getting good structures, you 
will have bad ones.


P.S. About not using water, I do not know. Any insights here?

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