[gmx-users] REMD functionalities

David spoel at xray.bmc.uu.se
Wed Nov 9 22:43:25 CET 2005

On Wed, 2005-11-09 at 21:27 +0100, pascal.baillod at epfl.ch wrote:
> Dear REMD developers,
> I would like to know if the REMD implementation in gmx-3.3 can do the following
> (or if extensions are planned):
> 1) Is there a per-replica trajectory analysis tool (i.e. creating a pseudo
> trajectory following a starting conformation along its MD at different
> temperatures)?
> 2) Additionnaly to 1), is there a tool to visualize schematically this
> "pseudo-trajectory" of a replica (with moves in temperature space)? Something like
We have some scripts that do this. We'll post them on the gromacs
website when they are good enough for general use.

>      _____
>     /     \
> ___/       \____
>                 \
>                  \____
> (where the slash and backslash show the MC move (swap) and the straight lines
> the md part)
> 2) NPT MD possible?
Yes. Necessary in most cases.
> 3) Can the potential energy of the solute only be used in the swapping
> probability function?
No. It wouldn't be hard to implement but it is useless in my opinion.
> 4) Is the current version NVT REMD? If so, dose it rescale the velocities of
> swapped replicas in function of a ration of temperatures?
Depends on whether you turn on P coupling or not.

> 5) How small can the REMD run length be set to, in the current version, and how
> dose this affects the relaxation of the potential energy of swapped
> conformations (i.e. is a new swap is attempted on non relaxed conformations)?
1 time step. This is your responsibility of course.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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