Thanks, Ross, for the fast response and solution.
And I found the problem with my system even without being able to
exactly reproduce :)
On 05/14/2013 01:35 PM, Ross Walker wrote:
> Hi Jan-Philip,
>
> This looks an oversight by someone. Here's the code:
>
> if (ntt .eq. 1) then
> write(mdout,'(/a)') 'Berendsen (weak-coupling) temperature
> regulation:'
> write(mdout,'(5x,3(a,f10.5))') 'temp0 =', temp0, &
> ', tempi =', tempi, ', tautp =', tautp
> else if (ntt .eq. 2) then
> write(mdout,'(/a)') 'Anderson (strong collision) temperature
> regulation:'
> write(mdout,'(5x,4(a,i8))') 'ig =', ig, ', vrand =', vrand
> write(mdout,'(5x,3(a,f10.5))') 'temp0 =', temp0, ', tempi =',
> tempi
> else if (ntt .eq. 3) then
> write(mdout,'(/a)') 'Langevin dynamics temperature regulation:'
> write(mdout,'(5x,4(a,i8))') 'ig =', ig
> write(mdout,'(5x,3(a,f10.5))') 'temp0 =', temp0, &
> ', tempi =', tempi,', gamma_ln=', gamma_ln
> end if
>
>
>
> So it ONLY prints ig if you are using a thermostat based on the random
> number stream. It does not appear to be smart enough to print it if you
> have ntt=0 or 1 but hot start your velocities with irest=0 and tempi>0.0.
>
> I'll fix it in the tree and we can issue a bug fix but for your sims there
> not much that can be done I'm afraid. Sorry.
>
> All the best
> Ross
>
>
>
> On 5/14/13 4:02 AM, "Jan-Philip Gehrcke" <jgehrcke.googlemail.com> wrote:
>
>> Hello,
>>
>> I am using pmemd.cuda for a "restart" run where initial velocities are
>> not read from the restart file but assigned randomly (ntx=1, irest=0)
>>from the Berendsen thermostat. The random seed is taken from the wall
>> clock (ig=-1).
>>
>> Now I have a problem in one run (step 26000: Etot=-136974.1332, step
>> 28000: Etot=NaN) and would like to reproduce with a smaller step size.
>>
>> From the mdout file I get:
>>
>> "Note: ig = -1. Setting random seed based on wallclock time in
>> microseconds."
>>
>> But I don't find the actual value used. I cannot reproduce the run with
>> the exact same set of initial velocities, right?
>>
>> Would you mind making this possible in the future?
>>
>> Thanks,
>>
>> Jan-Philip
>>
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>
>
>
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Received on Tue May 14 2013 - 05:30:04 PDT
