[gmx-users] to know about constraints

[Justin A. Lemkul]

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

-- 
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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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