[gmx-users] Fw: CAN'T CALCULATE THE ENERGY OF SYSTEM ONLY
jaswalradhika at yahoo.co.in
Fri Dec 26 10:05:44 CET 2008
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.
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