[gmx-users] Re: Re: segmentation fault while running eneconv

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Jan 26 14:37:17 CET 2011

Dear Justin,
thanks a lot for your suggestions. I checked the first 50ns simulation log
files and in fact they start at zero and they don't say Gromacs is using
checkpoints. Therefore, I'll follow your suggestions and discard the first
5ns simulations.
Just to be sure about it: to use checkpoints for the continuation of a MD
that has not crashed, are the followings the correct commands? (now I'm
writing in general)
tpbconv -s first_MD.tpr -extend desired_time_ps -o second_MD.tpr
mdrun -s second_MD.tpr -cpi first_MD.cpt -deffnm second_MD
I was quite sure about it...until yesterday...
Since I used the above format, if it is correct, the only other possibility
is that I made a mistake in writing the correct name of the 5ns .cpi file. I
see in the manual that if no checkpoint file is found, Gromacs restarts from
the first step of the .tpr file. Could it be possible that I wrongly wrote
the name of the .cpt file in the mdrun command and therefore Gromacs
restarted from the first step? If this hypothesis is true, I leave just a
little comment for developers: IMHO, it would be better if this option would
be less "intelligent" (this is the definition of the manual) and stop the
program claiming for the lack of the .cpt file, in case of such a mistake...
Thanks to all and best regards
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma, 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Email: anna.marabotti at isa.cnr.it
Skype account: annam1972
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with a gun is a dead
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