[gmx-users] REMD functionalities

[pascal.baillod at epfl.ch]

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
 
     _____
    /     \
___/       \____
                \
                 \____

(where the slash and backslash show the MC move (swap) and the straight lines
the md part)

2) NPT MD possible?

3) Can the potential energy of the solute only be used in the swapping
probability function?

4) Is the current version NVT REMD? If so, dose it rescale the velocities of
swapped replicas in function of a ration of temperatures?

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)?

Thank you very much for your information!

Pascal Baillod



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Pascal Baillod (PhD student) 
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Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	
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