[gmx-users] remd ... is it exchanging?

[David van der Spoel]

Carsten Baldauf wrote:
> dear all//
> i am trying to run remd simulations on a 16 residue peptide using 16 
> replicas in a temperature range from 275 to 419 kelvin.
> i follow the method described here: Seibert, M., Patriksson, A., Hess, 
> B., van der Spoel, D. Reproducible polypeptide folding and structure 
> prediction using molecular dynamics simulations. J. Mol. Biol. 
> 354:173–183, 2005.
> 
> when i look in the *log files is think i find the sections logging the 
> exchanges:
> Replica exchange at step 1000 time 2
> Repl 0 <-> 1 dE = 3.180e+01 dpV = 5.043e-04 d = 3.180e+01
> Repl ex 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
> Repl pr .00 .00 .00 .00 .00 .00 .00 .00
> 
> the line 'Repl pr ' allways only contains .00's. thus i guess there is 
> no exchange happening. am i right? what are the possible reasons and 
> what you suggest me to change?
> thanks a lot//
> carsten
> 
> 
> 
> 
yes. in the Seibert paper the number of atoms was very small < 4000. The 
number of replicas should be inversely proportional to the number of 
atoms, so if you have 16000 atoms you need 64 replicas to cover this 
T-range.

-- 
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://folding.bmc.uu.se
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