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<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>Dear
Justin,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>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.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>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)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>tpbconv -s
first_MD.tpr -extend desired_time_ps -o second_MD.tpr</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011>and</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>mdrun -s
second_MD.tpr -cpi first_MD.cpt -deffnm second_MD</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>I was quite sure
about it...until yesterday...</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>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...</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=140271613-26012011>Thanks to all and
best regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=140271613-26012011>Anna</SPAN></FONT></DIV>
<DIV align=left><FONT size=2
face=Arial>____________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science,
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino (Italy)</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Email: <A
href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web page: <A
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with a gun is a dead man"</FONT></DIV>
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