[gmx-users] Free Energy Change of Dihedral Restraints.
Mark Abraham
mark.j.abraham at gmail.com
Wed Jan 23 16:24:27 CET 2019
Hi,
See
https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/topol.top#L24801
which
implements
https://github.com/gromacs/regressiontests/blob/master/freeenergy/restraints/grompp.mdp#L291
Mark
On Wed, 23 Jan 2019 at 13:14 Drew <andrew.pearce13 at imperial.ac.uk> wrote:
> Hi all,
>
> I'm trying to perform a free energy calculation to understand the impact
> of some dihedral restraints I am using to ensure planarisation of the
> backbone of some oligomers I am working on. I've previously done a fair
> few Free Energy of Solvation calculations and I had noticed that there
> exists the option of using restraint-lambdas however I'm having trouble
> getting it to work.
>
> I had assumed I could include the line in the MDP file:
>
> restraint_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
>
> and it would modify the dihedral_restraints element of the topology file.
>
> [ dihedral_restraints ]
> ; ai aj ak al type label phi dphi kfac power
> 15 10 70 75 1 180 0 1000
> 11 10 70 71 1 180 0 1000
> 80 79 139 140 1 180 0 1000
> 84 79 139 144 1 180 0 1000
> 153 148 208 213 1 180 0 1000
> 149 148 208 209 1 180 0 1000
> 218 217 277 278 1 180 0 1000
> 222 217 277 282 1 180 0 1000
> 291 286 346 351 1 180 0 1000
> 287 286 346 347 1 180 0 1000
> 356 355 415 416 1 180 0 1000
> 360 355 415 420 1 180 0 1000
> 429 424 484 489 1 180 0 1000
> 425 424 484 485 1 180 0 1000
>
> So that as we move from Lambda=0 to 1 all the restraints go from off to on.
>
> When I run the calculation I get the Warning:/"The lambda=0 and lambda=1
> states for coupling are identical"./
>
> I've scoured the gmx-users archive and I think I need to use the pull
> commands in addition to the free-energy ones (pull-coord1-k and
> pull-coord1-kB) to set what state 0 and state 1 is but I can't seem to
> get that to work. The other option I can think of is to change kfac
> myself for each of those Lambdas and the do the thermodynamic
> integration myself but I'd feel a bit lost about how to do that.
>
> Any help or advice would be much appreciated!
>
> Thanks in advance,
>
> Drew
>
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