[gmx-users] simulation with position constraint by a harmonic potential

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 26 23:56:18 CEST 2011

Liu, Liang wrote:
> Firstly I want to thank for your reply, yes, it should be position 
> restraint.
> I don't know how to reply in the thread, actually that was my first 
> post. Therefore I have to ask you here, hope it also work to you.

Simply reply to the message.  The discussion needs to stay on the list.  The 
members are not private tutors.

> My question is how to perform a position restraint simulation with the 
> heavy atom constrained to its initial position by a harmonic potential 
> E=k(r-r0)^2,
> which changes with k equal to 0, 10, 20, ..., 90, 100, and so on?

You can adjust the force constant in the posre.itp file.  There is no automated 
way of decreasing or increasing a restraint; independent simulations must be run 
on the different topologies.


> Thanks, and any helps will be highly appreciated.
> -- 
> Best,
> Liang Liu


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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