Hi Jesper,
Yes that would be my suggestion as well. Either save all your restarts or
just use the frames in the trajectory file. You 'should' be able to pass
these into sander using imin=5 and calculate the pressure for each frame -
I think... You'll need to try it and see (it may need some code tweaking)
but one should be able to get sander to calculate you the pressure for
each frame in a trajectory file.
All the best
Ross
On 11/5/14, 11:23 AM, "Scott Le Grand" <varelse2005.gmail.com> wrote:
>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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>> > AMBER mailing list
>> > AMBER.ambermd.org
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>>
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Received on Wed Nov 05 2014 - 11:00:02 PST
