[gmx-users] how to fixe distance

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 12 23:06:48 CET 2011

najwa drici wrote:
> hi all
> How can I fix some distances and angles in manner, that I can set up 
> long molecular dynamic simulation without structural lost?

Read in the manual about distance, angle, and/or dihedral restraints.

If you're having problems with secondary structure changes, there are a whole 
host of reasons it might be erroneously happening, including, but not limited 
to, force field limitations and incorrect .mdp settings (i.e. incorrect use of a 
given force field).  So before you go trying to force a certain behavior, be 
sure you understand the reasons something might be happening.


> cordially
> DRICI nedjoua


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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