[gmx-users] remd ... is it exchanging?
carsten.baldauf at biotec.tu-dresden.de
Mon Aug 28 17:27:20 CEST 2006
i never used pymol ... in your paper you write you solvated using pymol.
is it a plugin or or a standard feature? can you give me a hint how to
David van der Spoel wrote:
> 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//
> 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.
dr carsten baldauf
biotechnologisches zentrum der tu dresden
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