[gmx-users] energy monitoring

Ghermes Chilov Ghermes at belozersky.msu.ru
Sun Nov 24 08:46:32 CET 2002


>>>B: Are there any limitations on the string size in the .mdp file?
>>>Namely, if we have a lot of energygroups (say 200 aminoacids and 1
>>>ligand) and we wish to skip dynamics of the first 200 groups by
>>>freezing them, how can we add 200x200 entries into string
>>>'freezegrps'? I mean, can the program accept such a long string?
>>No. You will have to modify gmx/src/kernel/readir.c 
>>You can not have more than 256 groups, unless you modify the type that
>>holds the groups (in atoms and mdatoms structures)
EL> And, as it says in the manual: things will get considerably slower with 
EL> that many energy groups.
EL> Unless you have a _very_ good reason for using 200 separate groups, it's 
EL> a much better idea
EL> to define a small number of groups for your simulation and then possibly 
EL> rerunning the energy
EL> calculation on the trajectory (using frames spaced 1 ps apart or something).

Thanks for fruitful ideas! We'll check both of them.

However, to define a smaller number of groups means to forsee the
answer, i.e. to know the patterns in the protein that govern the
substrate binding... I wish we could crack it! :-)))


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