[gmx-developers] Computing prot pot ener in the gmx code

[Anton Feenstra]

Mark Abraham wrote:
> Yang Ye wrote:
> 
>> pascal.baillod at epfl.ch wrote:
>>
>>> Thank you very much David, thank you very much Mark!
>>> I actually already have a gromacs REMD implementation, that is an 
>>> external
>>> script which iteratively lauches jobs, computes protein potential 
>>> energies (by
>>> summing terms obtained with g_energy protein energy group output), 
>>> computes swap
>>> probabilities in fct of these energies, dose the possible swaps and 
>>> relaunches
>>> the new runs. But that is of course rather slow, as a call for grompp is
>>> necessary every new run.
>>> 1) Would there be a way to bypass grompp in the context of the 
>>> external script?
> 
> 
> Where no exchange has occured, you can use tpbconv -extend to convert 
> the previous .tpr file... the only change you want is a new end run time 
> and it does that nicely. To speed things up, you can of course decrease 
> the frequency of exchange attempts, and maybe run g_energy & grompp in a 
> distributed fashion manually.

Or, your could work with the ascii topology format (tpa), and have the 
script hack that directly (yes it is dirty, and you'll have to be *very* 
careful!). Due to the huge amount of text-IO I'm not sure if it will be 
much faster than re-running grompp.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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