From: matthew reeves (mreeves94_at_gmail.com)
Date: Tue Dec 06 2016 - 13:16:00 CST
I’ve run several NAMD simulations on a short chained molecule which each simulation using a different sized water box. I can’t help but noticing that in the .log file produced at the end of each simulation the energy values change quite considerably. This implies that NAMD outputs the energy of the whole system (including the water molecules) as opposed to the just the molecule of interest. Is there a way to get the energy values of just the solvated molecule and not the water included?
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