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
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 14 2013 - 05:00:02 PDT
