[gmx-users] Free Energy Change of Dihedral Restraints.

[Mark Abraham]

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
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.