[gmx-users] Harmonic restraint in FEP

[Justin Lemkul]

On 7/13/16 3:52 PM, Alexander Alexander wrote:
> Dear Gromacs user,
>
> To avoid conformational changes of a single amino acid while it is
> perturbed (vdW and q --> 0) in Free energy calculation, I need to apply a
> harmonic restraints on(or between?) some of it's atoms by [
> distance_restraints ] and "restraint-lambdas".
>
> First of all, is this right? I means " "restraint-lambdas" can be used for [
> distance_restraints ]?
>

No.  You can only modulate dihedral restraints and the pull code (which is what 
you should be using anyway):

http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#free-energy-calculations

> If so, how can I find out proper "low, up1, up2 and fac" for a molecule?
>
> One more question is that what the "restraint-lambdas" should be look like
> when harmonic restraints is going to be applied(turning on gradually) by
> whatever method?
>
>
> restraint-lambdas   = 1.0 0.8 0.6 0.4 0.2 0.0
> OR
> restraint-lambdas   = 0.0 0.2 0.4 0.6 0.8 1.0
>

See available options in 
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#com-pulling

The A-state is 0 and the B-state is 1.  The behavior of restraint-lambdas 
depends on how you choose/need to set up the restraints themselves.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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