[gmx-users] Switching Group to Verlet

[Mark Abraham]

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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