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

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 26 14:45:43 CET 2011

Anna Marabotti wrote:
> 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
> and
> mdrun -s second_MD.tpr -cpi first_MD.cpt -deffnm second_MD

A bit redundant ("mdrun -deffnm second_MD -ci first_MD.cpt" is all you need), 
but yes, correct.

> I was quite sure about it...until yesterday...

That's why writing scripts to execute your commands is a good idea.  You have an 
absolute record of what you typed.

> 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...

True, if mdrun can't find your .cpt file, it starts the run from the beginning 
time in the .tpr file.  I believe there may have been some relevant changes in 
the 4.5.x series (i.e. stopping when files are missing), but I think that's more 
related to the fact that, as of version 4.5, mdrun -append is the default behavior.


> Thanks to all and best regards
> Anna
> ____________________________________________________
> 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 <mailto: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 man"


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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