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 Sat May 31 2014 - 09:00:02 PDT
