Dear Friends,
While running POPC bilayer simulation in AMBER14 (LIPID14, pmemd.cuda),
I found very different Area per head group (APH) using two
different barostat. I ran two identical lipid (64 lipid per leaflet)
system.
I see very less APH for MC babrostat (61.2) as compared to Berendsen
barostat(~65.3 A) during the course of simulation. The berendson barostat
seems to reproduce the APH reported in Lipid14 force-field paper but not
the MC barostat.
Is it expected ? Please refer to the attached figure for the variation of
APH with simulation time. Rest of the input parameters are exactly similar
except the barostat for both the systems. I follow the procedure given in
the tutorial by Benjamin Madej and Ross Walker on the official AMBER
website to do the simulation.
Another thing I observed (in lipid +complex system) that if I use NTR=1
option (Rest input parameter similar to tutorial) to restrain the system
during the equilibration, the simulations are not stable.
Can you please comment on above issues.
Thanks for the kind concern.
--
*With Regards,HIMANSHU JOSHI Graduate Scholar, Center for Condense Matter
TheoryDepartment of Physics IISc.,Bangalore India 560012*
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Received on Fri Nov 13 2015 - 04:00:04 PST
