Hi Joshi,
Yes we have seen similar behavior with the MC barostat vs Berendsen and are still looking into it to figure out what is going on. We think it is related to the use of anisotropic boundary with the MC barostat. For now the suggestion is to stick with the Berendsen barostat for Lipid bilayer simulations.
With regards to the NTR=1 question - can you provide more details please. Your mdin and mdout files and also the command lines you are using for each stage of the run would be helpful.
All the best
Ross
> On Nov 13, 2015, at 3:42 AM, Himanshu Joshi <himanshuphy87.gmail.com> wrote:
>
> 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 - 09:30:04 PST
