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

Leontyev Igor ileontyev at ucdavis.edu
Thu May 28 06:24:59 CEST 2009

>> 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).

>> 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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