[gmx-developers] Re:Re: energy calculation fails in "-rerun" mode

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 28 07:20:06 CEST 2009

Leontyev Igor wrote:
>>> The problem appears when I am trying to recalculate energies and dhdl
>>> values
>>> using "-rerun" option.
>> There were bugfixes for -rerun between 4.0.4 and 4.0.5. Please check
>> release notes for this sort of thing :-) I don't know if you might still
>> have a real issue, but please update to 4.0.5 and try again.
> The upgrade to 4.0.5 version fixed issues 2) and 3), but still the 
> average values are not printed at the end of the log-file (see the issue 
> 1).

I think that's intended as a feature, rather than a bug, e.g. 
http://www.gromacs.org/pipermail/gmx-commit/2009-May/001656.html. I 
don't know of a good reason either way. You can get the data you want 
from g_energy on the .edr file, of course.


>>> Recalculated values do not coincide with original
>>> (from MD run) values. The difference is definitely larger then the
>>> uncertainty due to trajectory rounding (trajectory precision is 3 
>>> digits).
>> Unless you did neighbour-searching every step of your original
>> trajectory, then you will likely get different results, since nstlist !=
>> 0 implies neighbour searching every step for reruns.
>> Mark
>>> Trajectory has been obtained for the solute (Cl+,CL-) immersed in the
>>> polarizable solvent (benzene).  The solvent is modeled by the 
>>> polarizable
>>> Drude oscillator model. Shell particles are used for benzene 
>>> molecules. The
>>> "rerun" procedure results to a strange output.
>>> 1) Average values are not printed out at the end of the log-file. 
>>> There is
>>> only some message at the beginning: "Will not sum the energies at every
>>> step, therefore the energy file does not contain exact averages and
>>> fluctuations."
>>> But I didn't turn on the option -nosum.
>>> 2) Output energies are not updated for each configuration of my 
>>> trajectory,
>>> but only once per 20 snapshots, i.e. 20 consequent configurations have
>>> exactly the same energies.
>>> The points 1) and 2) seems to be related. There is also question 
>>> regarding
>>> minimization of the shell particle positions in "-rerun" mode.
>>> 3) My trajectory already have minimized (during MD) shell positions. 
>>> I only
>>> need to calculate energies corresponding to a given configuration,
>>> therefore, I don't need minimize the shell particles. How can I turn off
>>> the
>>> minimization in "-rerun" mode? I tried to specify "niter=0", but it 
>>> results
>>> to a strange output (unphysically large forces which are increased on 
>>> each
>>> step). Below is my mdp- and log-files: 
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