[gmx-users] angle/distance/position restraints in alchemical free energy calculation

[Justin Lemkul]

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 (
>> http://pubs.acs.org/doi/pdf/10.1021/jp0217839).
>> 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:

http://charmm-gui.org/?doc=input/gbinding

The protocol is described in full in 
http://pubs.acs.org/doi/abs/10.1021/ci300505n

-Justin

>
>> 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.
>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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