[gmx-users] REMD functionalities

[David]

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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++