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

[Carsten Baldauf]

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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