[gmx-users] remd ... is it exchanging?
Mark.Abraham at anu.edu.au
Tue Aug 29 04:15:20 CEST 2006
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
> 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?
Yep. You will see "x" between pairs of numbers in the "Repl ex" line
when exchange occured successfully between those pairs. You can
experiment with making your temperature gaps smaller to get a feel for
how close they need to be for your size of system.
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