[gmx-users] angle/distance/position restraints in alchemical free energy calculation
jalemkul at vt.edu
Fri Nov 3 14:39:38 CET 2017
On 11/3/17 9:36 AM, Wes Barnett wrote:
> On Fri, Nov 3, 2017 at 2:00 AM, minky son <minky0710 at gmail.com> wrote:
>> Dear gmx user,
>> I’m studying about alchemical free energy calculation.
>> I have been read some articles about restraints during free energy
>> calculation, they referred the procedure in the article (
>> I tried to search mailing list, but still I couldn’t understand.
> I don't see any indication in that article of the researchers using
> GROMACS. It looks like they are using CHARMM.
And to make it really simple:
The protocol is described in full in
>> The manual said “restraint-lambdas” option only handle dihedral
>> restraints, and the pull code restraints
>> How to apply angle/distance/position restraints with respect to lambda?
> I don't believe those other restraints can be coupled for free energy
> changes in GROMACS at this time.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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