Hi All,
In my study, I am trying to see the membrane penetrating behavior of few
peptides. As a control, I took the peptide which is well known to cross the
membrane. I prepared the peptide structure (20 amino acid long ) and 20 ns
simulation to get the stable conformation. Now I prepared the membrane
(POPC) and kept the peptide over the membrane (using VMD). I generated the
lipid parameters using AM1-BCC method and then performed the simulation
(minimization, heating, equilibration.)
Now during simulation the peptide goes away ( within ns) from the lipid
membrane and it never comes back ( during simulation of 20ns).
I guess there is no point of continuing the simulation ? Can you please
help me to get rid of this issue.
Thanks,
HM
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Received on Tue Jan 15 2013 - 09:30:03 PST
