From: Jacopo Sgrignani (sgrigna_at_sissa.it)
Date: Thu Sep 15 2011 - 07:12:26 CDT
I'm performing SMD simulations and I have a question about the force applied
to pull out a ligand from a protein.
Actually, analyzing the results of my simulations, they seem correct and the
directions of the ligand exit are consistent with
the directions I have specified in the input file.
However for one of the 4 simulations, during the first 300 ps, the force
applied is negative.
What does it mean?
I think this is the favoured exit pathway, however I would like to be sure
that it has a physical meaning, and that It is not related with my tecnical
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