ok, i got it wrong ...
i see now my problem ... i am using an extremely big box ...
the length of my fully extended peptide is about 5.6 nm i will try a box
with an image distance of 5.7 nm.
this should more or less resemble the status of your input, am i right?
thanks for the help//
carsten
David van der Spoel wrote:
Carsten Baldauf wrote:
dear david//
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 do it?
It doesn't write that... We used pymol (pymol.sf.net) to generate the
starting structure of our peptide. Genbox was used for solvation.
thanks//
carsten
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//
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.
--
dr carsten baldauf
biotechnologisches zentrum der tu dresden
http://www.biotec.tu-dresden.de/pisabarro
http://www.biotec.tu-dresden.de/~carstenb
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