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

[David van der Spoel]

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.
>>
> 
> 


-- 
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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