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.
-Justin
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.marabo...@isa.cnr.it <mailto:anna.marabo...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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