Hi,
I am minimizing a protein in water, using explicit solvent. I'm following the input files of the tutorial 1, part 3/4. Except, i am applying it to a protein.
The vacuum minimization works fine, in that RMS stabilizes and EP tot decreases and stabilizes. However, for the water explicit minimizations, the RMS shoots off to high values, in a smooth continually increasing fashion. I am using the result of vacuum simulation PDB as the input for all my water simulations (i am first fixing the protein, the removing restraints, per the tutorial).
I am plotting potential energy and RMS during the simulation. The PE initially spiked up, but now it's is decreasing and stabilizing (at a highly negative value). The RMS, however, continues to rise.
Does this always mean there is something wrong with my simulation? Or do I have to make movies of the files to be sure? If it means something is wrong, how do i decide what to change to make it right?
Thank you,
Sonya Dave'
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Received on Wed Oct 18 2006 - 06:07:28 PDT
