Not an AMBER user. My expertise is on LAMMPS.
Have you tried using LAMMPS.
You can extract the pressure tensor from the trajectories and compute
autocorrelation using a custom code.
Also pressure tensor can be very very noisy for finite sized systems. You
must use large number of replicas to obtain reliable answer.
Arun
www.arunsrikanth.com
On Fri, Oct 12, 2018 at 7:57 AM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Oct 09, 2018, Lorenzo Gontrani wrote:
>
> > Dear amber gurus, I am currently facing the problem of calculating
> > viscosity from MD trajectories.
> >
> > Is there any "simple" way of obtaining the pressure tensor trajectory to
> > calculate system viscosity through Green Kubo relations?
>
> I was waiting for someone else to (perhaps) chime in. But I'm not aware
> of anything like this in the code now: you would probably have to modify
> things to output the pressure tensor to a file, and do some
> post-processing.
>
> ....dac
>
>
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Received on Fri Oct 12 2018 - 11:00:03 PDT
