David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 26 10:09:58 CET 2008

radhika jaswal wrote:
>     Respected Sir,
>     As u suggested I did the same, but I was unable to calculate it. I
>     used make_ndx in which I selected protein and then I used with
>     grompp with -n option but the energy it is showing is of the whole
>     system not of the protein only.
>     To mke it clear suppose if I have a protein A and solvent system B.
>     I want to simulate the system A + B but I want the energy of A
>     separately with the co-ordinates of A as in A + B and then energy of
>     B with its original co-ordinates in A + B as I want to compare the
>     different conformational states of a protein because editconf or
>     genbox adds unequal number of water molecules. OR I have a method to
>     add same number of water molecules to every state as water molecules
>     which are not interacting also contribute towards energy parameter.
>     Radhika
how do you define the energy of just the protein if it is in solvent?

genbox -maxsol XX gives you at most XX waters.

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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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