[gmx-users] Switching Group to Verlet

[Mahmood Naderan]

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