[gmx-users] Switching Group to Verlet

[Mahmood Naderan]

OK thanks for the clarification.


Regards,
Mahmood



On Sun, Oct 23, 2016 at 1:29 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I've said before that this is not a problem. Imagine you suppressed all
> 20000 step outputs that wrote 80 characters of output each. That's 1.6 MB,
> which you could also suppress by piping terminal output to /dev/null. The
> minimization ran in around 100 seconds, so the load on the infrastructure
> was under 20 kb/sec. Can you name any workload on the cluster that produces
> less traffic?
>
> Mark
>
> On Sun, 23 Oct 2016 11:12 Mahmood Naderan <mahmood.nt at gmail.com> wrote:
>
> > Hi Mark,
> > So I changed the code (gromacs-5.1/src/gromacs/mdlib/minimize.cpp) like
> > this:
> >
> >
> >         if (MASTER(cr))
> >         {
> >             if (bVerbose && ((++myCounter)%10000==0))
> >             {
> >                 fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e
> > Fmax= %11.5e, atom= %d%c",
> >                         count, ustep, s_try->epot, s_try->fmax,
> > s_try->a_fmax+1,
> >                         ( (count == 0) || (s_try->epot < s_min->epot) ) ?
> > '\n' : '\r');
> >       ...
> >
> >
> > myCounter is similar to the variable count. Where count has been
> > initialized or incremented, I also did that for myCounter.
> >
> > But this doesn't work! After a minute (where is the step is much more
> than
> > 10000) the program terminates
> >
> >
> >
> > Steepest Descents:
> >    Tolerance (Fmax)   =  1.00000e+01
> >    Number of steps    =        20000
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 10 (which may not be possible for your
> system).
> > It
> > stopped because the algorithm tried to make a new step whose size was too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> >
> >
> >
> > Regards,
> > Mahmood
> > --
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