[gmx-users] Restraining atoms

[Justin A. Lemkul]

On 5/9/12 11:34 AM, Steven Neumann wrote:
> Dear Gmx Users,
>
> My plane surface is made of atoms. I would like to restrain positions between
> them so they will move all togehter or create bonds between them. Would you
> advise how to do this in the easiest way?
>

If you need to "restrain positions" then you need [position_restraints].  The 
form of the restraints follows from the structure of the topology.

Also note that you cannot create bonds in a classical MD simulation.  If you 
need to maintain some distances, then use actual bonds or [distance_restraints].

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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