On 6/19/12 1:28 PM, Anik Sen wrote:
Dear gromacs developers,
This is Anik. For a certain work with
nonbonded interactions with alkali halides and water, I need to constrain some
specific atoms in the energy minimization step. Is there any option to constrain
the atoms in a specific calculation. The water molecules and other atoms may be
in movement during the calculation.
I think what you're looking for are "restraints," not "constraints." Restraints
inhibit motion; constraints fix bond lengths or angles.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
Position restraints are a common part of many workflows. These are likely what
you need.
http://www.gromacs.org/Documentation/How-tos/Position_Restraints
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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