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

[Mark Abraham]

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.

Mark