[gmx-users] energy monitoring

Erik Lindahl erik at theophys.kth.se
Sat Nov 23 16:22:38 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)
And, as it says in the manual: things will get considerably slower with 
that many energy groups.
Unless you have a _very_ good reason for using 200 separate groups, it's 
a much better idea
to define a small number of groups for your simulation and then possibly 
rerunning the energy
calculation on the trajectory (using frames spaced 1 ps apart or something).



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