Thanks Jason
On May 31, 2014, at 11:51 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 Sat May 31 2014 - 09:30:02 PDT
