[gmx-developers] Position Restraints in Thermodynamic Integration

Berk Hess hess at kth.se
Wed Sep 27 22:04:50 CEST 2017


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:
> Hi,
> 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.
> Best,
> James
> ________________________________________
> 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
> Hi,
> 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.
> Cheers,
> Berk
> On 27/09/17 14:46 , Carruthers, James wrote:
>> Hello,
>> In the online user guide for 2016.4 it states in mdp options that the restraint-lambdas directive only controls dihedral and pull code restraints. However, the 2016.4 manual states that position restraints can be interpolated for free energy calculations (pp. 137,138). I would like to be able to control position restraints as this will enable a convenient way to implement the Einstein crystal method of calculating solid state chemical potentials. This raises two questions, is there a technical reason why restraint-lambdas is restricted to controlling only those two parameters and is there a way to implement scaling position restraints outside of the *-lambdas framework that can be analysed by gmx bar?
>> Best regards,
>> James
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