[gmx-developers] inconsistent logfiles

[Anton Feenstra]

Vibin R wrote:
> 
> Hi
>         While doing energy minimisation with different initial structures,
> I am getting different starting points (such as sometimes step0,
> sometimes step1, step4 etc) both from energy trajectory and from the
> logfile)
> 1. What could be the reason, why i am not getting step 0,1,2,...etc
> consistently. What should i do for getting it?
> 2. Will it be meaningful if i assume that the step0 energy values which we
> get from the logfile as the energy of the structure prior to energy
> minimisation?

em only records those steps that were successful, i.e. have lower
energy than the previous step. Actually, I think step -1 is the
starting structure per se, step 0 already has the bonds constrained
(if constraints are turned on). Possibly running mdrun -v will get
you more output on screen, but I am not sure about the file output.

-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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