[gmx-users] mdrun -rerun question

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Tue Dec 16 11:02:01 CET 2003

On Tue, 16 Dec 2003, Michael Shirts wrote:

> I'm trying to understand what the -rerun option does exactly.
> So, here's my problem.  I ran mdrun, outputting a .trr with coordinates every
> 500 steps (0.002 ps step length, 100 ps total).  I then used g_energy and the
> .edr file to generate an .xvg with a number of observables (listed below).  I
> then ran a mdrun -rerun using the output .trr file, generating a new .edr
> file, and a new .xvg.  All programs were run complied in double precision.  I
> then took the difference between the numbers in the two files, and got the
> following results.  Why any difference?  Shouldn't it produce the same
> energies?
> Some particularly odd things -- why is the box length different between the
> two .edrs?  If it's just taking snapshots, the box should be the same at every
> step.  Instead, there's a difference.  Secondly, the differences are multiples
> of the same number, which is some negative power of two.  For example, in the
> LJ energy column, all energies are different by multiples of 1/2048.  In the
> short range coulomb column, the multiples appear to be of 1/512 (I'm just
> giving the first 20 here - I generated 100 ps worth).  Only the box length
> (and therefore the dispersion correction, which is proportional to the volume,
> and the potential energy, which includes the dispcorr) isn't following this
> pattern.  Is this an artifact of the .edr format?  If so, why is it appearing
> at such a low resolution?  The total LJ energy is approximately 6000 kJ/mol,
> so these errors are of order 10^-6 or 10^-7, much too low for double
> precision.  And why is it different, if it's going through the same energy
> routines?  I guess I could understnd some sort of rounding error for the
> energies, but the box size error is of order 10^-4; a box problem I might
> account for the energy differences, too, as the total energies would change as
> the periodic boundary conditions change.
> Any suggestions?
> Also, the "averages" output of g_energy from a rerun file are incorrect, as
> they appear to have the numerator of the coordinate output frequency, but the
> denominator of the original run, giving incorrect averages for these
> snapshops.
> Thanks,
> Michael Shirts

Did you use the same mdp file for both run? if that is the case, you have
to set


in the mdp used for the rerun.

Otherwise, I don't know the reason!


More information about the gromacs.org_gmx-users mailing list