Dear gmx users,
I'm trying to simulate membrane penetration with peptide(octamer) using
GROMACS-5.1.2. and I referred the Umbrella Sampling tutorial by Dr. Justin
After 100 ps umbrella_NPT run, peptides confirmations are still kept in
their initial coordinates. However, after 10ns of umbrella_MD, I cannot get
reliable results for WHAM analysis because the confirmations are quite
deviated from the umbrella_NPT structures.
(plz, refer two results,
So, my question is should I have to use position restraint for moving
ligands? or just extend simulation time for umbrella_NPT to get equilibrium
structures for umbrella_MD?
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