[gmx-users] Tricky implementation of REST in GROMACS 4.6.5

[Mark Abraham]

On Wed, Nov 19, 2014 at 10:38 AM, Carlo Martinotti <
carlo.martinotti at studenti.unimi.it> wrote:

> Thank you Justin,unfortunatly i tried to use your solution, but there are
> some problems with free energy use in REST. The first is that free energy
> interpolate from state A to state B, but can't manage to interpolate proper
> multiple dihedrals,


You can't change the multiplicity, but there's no reason you can't change
the other dihedral parameters between states, per Table 5.5 in the manual.

so i don't know how to treat dihedrals with this approach. The second and
> more trivial problem is that free energy isn't compatible with Verlet
> cutoff scheme, which pose various problems to me.
>

This works in Gromacs 5.


> But would it be that bad to use the methodology i described?


I would say it's not bad, but I would use a smaller T increment. You only
need to fool it into realising T and T+deltaT are different. 32 replicas
times 0.1K is a larger total range of T than you need to use.

Mark

--
> 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.
>