Why don't you just periodically dump a restart file and calculate the
pressure from that with a separate process?
On Wed, Nov 5, 2014 at 10:18 AM, Sorensen, Jesper <jesorensen.ucsd.edu>
wrote:
> Hi Jason,
>
> I’d like to follow up on this… Is there a way in post-processing to
> recalculate the pressure?
>
> I set the pressure with the Berendsen barostat first before switching to
> MC, so I imagine that it’s where I’d like it to be on average (I realize it
> fluctuates a lot), but it’d still be nice to check that it hasn’t diverged
> too much due to unforeseen events…
>
> Is it not possible to asynchronously compute the virial for the energy
> output using pmemd.cuda maybe by throwing it to the CPU similar to writing
> files? This way the simulation can proceed, keeping it’s efficient speed,
> yet outputting this property similar to the Berendsen barostat… I guess
> this would also be a good question for Ross Walker since it involves the
> GPU version of pmemd.
>
> Best,
> Jesper
>
>
> > On May 31, 2014, at 8:51 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> >
> > O
> >
> > n Sat, May 31, 2014 at 11:10 AM, Asaminew Haile <ashaethio.gmail.com>
> wrote:
> >
> >>
> >> Dear Amber Users
> >> I’m running MD with pmemd.cuda with barostat=2 option for pressure
> >> control, but in my energy output pressure is
> >>
> >> printed out as 0.0 as shown bellow
> >>
> >>> NSTEP = 100000 TIME(PS) = 12670.000 TEMP(K) = 302.51 PRESS =
> >> 0.0
> >>
> >>>
> >>
> >>> NSTEP = 200000 TIME(PS) = 12870.000 TEMP(K) = 299.32 PRESS =
> >> 0.0
> >>
> >>>
> >>
> >>> NSTEP = 300000 TIME(PS) = 13070.000 TEMP(K) = 301.04 PRESS =
> >> 0.0
> >>
> >>>
> >>
> >>> NSTEP = 400000 TIME(PS) = 13270.000 TEMP(K) = 301.09 PRESS =
> >> 0.0
> >>
> >>>
> >>
> >>> and also damped the following kind of warning information into the
> output
> >>
> >>> | Attempting MC barostat change: Failed
> >>
> >>>
> >>
> >>> | Attempting MC barostat change: Succeeded
> >>
> >>>
> >>
> >>> | Attempting MC barostat change: Failed
> >>
> >>>
> >>
> >>> | Attempting MC barostat change: Failed
> >>
> >>>
> >>
> >>> | Attempting MC barostat change: Succeeded
> >>
> >>>
> >>
> >>> | Attempting MC barostat change: Failed
> >>
> >>>
> >>
> >>> | Attempting MC barostat change: Failed
> >>
> >>>
> >>
> >>> | Attempting MC barostat change: Succeeded
> >>
> >>>
> >>
> >>> Any idea
> >>
> >
> > This is because pmemd.cuda does not compute the virial when using the MC
> > Barostat. Computing the virial is expensive (results in ~10-20%
> > performance reduction on GPUs compared to _not_ computing the virial).
> One
> > of the great things about the MC barostat is that the virial is not
> needed
> > (which is why ntp=1 or 2 with barostat=2 gives approximately the same
> > performance as NVT, whereas barostat=1 is significantly slower).
> >
> > The MC barostat in sander _does_ compute the virial and report the
> pressure
> > if those values are important to you.
> >
> > Hope this helps,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
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Received on Wed Nov 05 2014 - 10:30:03 PST
