[gmx-developers] Position Restraints in Thermodynamic Integration
j.carruthers2 at lancaster.ac.uk
Thu Sep 28 15:24:04 CEST 2017
Forgive my inexperience, I thought the restraints etc. were handled in the same way as the LJ and electrostatic interactions (i.e. couple-lambda0 and 1). I've gone through my topology and added explicit B state parameters and it's working as intended. Perhaps it would be worth emphasising in the online documentation that B parameters are only automatically generated for coulombic and vdW interactions.
From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of Berk Hess [hess at kth.se]
Sent: 27 September 2017 21:04
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] Position Restraints in Thermodynamic Integration
But the position-restraint code really seems to use the restraint lambda.
Are you using normal position-restraints and not flat-bottomed ones?
Have you set the position restraint force constants to zero in either
the A or B state?
On 09/27/2017 06:11 PM, Carruthers, James wrote:
> I just tried it at 0.0, 0.5 and 1.0 restraint lambdas. Position restraints are fully applied in all states and DH/Dlambda is effectively zero when the foreign lambdas only have different restraint-lambdas.
> From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of Berk Hess [hess at kth.se]
> Sent: 27 September 2017 13:59
> To: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] Position Restraints in Thermodynamic Integration
> Looking at the code position restraints are controlled through the
> restraint lambda. Have you actually tried it?
> This does mean the manual needs to be updated.
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