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<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>Dear
all,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=515392109-25012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>I launched on my
system a first simulation of 5 ns, then I prolonged it to 50 ns using
</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>tpbconv -s
tpr1_5ns.tpr -until 50000 -o tpr2_50ns.tpr</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>and then
</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>mdrun -s
tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>Since my simulation
was interrupted several times, every time I relaunched it simply
doing:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>mdrun -s
tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=515392109-25012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>At the end of these
simulations I obtained the following files:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>- md1_5ns.xtc and
.edr: files obtained from the first MD of 5 ns long</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>- md2_50ns.xtc and
.edr: files obtained by prolonging the first MD until 50ns</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>- md2_50ns_2.xtc and
.edr: files obtained by restarting the previous dynamics that was interrupted
before 50 ns</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>- md2_50ns_3.xtc and
.edr: same as before</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>- md2_50ns_4.xtc and
.edr: same as before</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=515392109-25012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>After all these
runs, I want to concatenate all the dynamics in order to have a single .xtc file
md_50ns_tot and a single .edr file md_50ns_tot.edr. For the first, I
used:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>trjcat -f
md1_5ns.xtc md2_50ns.xtc md2_50ns_2.xtc md2_50ns_3.xtc md2_50ns_4.xtc -o
md_50ns_tot.xtc</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>and all worked fine:
I obtained the output file with no errors (there are no errors also in the .log
files)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=515392109-25012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>On the contrary,
when I tried to do the same with eneconv:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>eneconv -f
md1_5ns.edr md2_50ns.edr md2_50ns_2.edr md2_50ns_3.edr md2_50ns_4.edr -o
md_50ns_tot.edr</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>I obtained the
following output:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=515392109-25012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>Opened
2GH9openmod4_pH10_5ns.edr as double precision energy file<BR>Reading energy
frame 1 time 100.000<BR>Opened
2GH9openmod4_pH10_50ns.edr as double precision energy file<BR>Reading energy
frame 0 time 0.000<BR>Opened
2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file<BR>Reading
energy frame 0 time 14900.000<BR>Opened
2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file<BR>Reading
energy frame 0 time 27800.000<BR>Opened
2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file<BR>Reading
energy frame 0 time 38800.000</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>Summary of files and
start times used:</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=515392109-25012011>
File
Start
time<BR>-----------------------------------------<BR>2GH9openmod4_pH10_5ns.edr
0.000<BR>2GH9openmod4_pH10_50ns.edr
0.000<BR>2GH9openmod4_pH10_50ns_2.part0002.edr
14900.000<BR>2GH9openmod4_pH10_50ns_3.part0003.edr
27800.000<BR>2GH9openmod4_pH10_50ns_4.part0004.edr
38800.000</SPAN></FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>Opened
2GH9openmod4_pH10_5ns.edr as double precision energy file<BR>Segmentation
fault<BR></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>Looking for some
hints in the gmx-users list the only thing I found that could be similar to my
problem is this old message:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011><A
href="http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html">http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html</A></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=515392109-25012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>I see in the output
error message that the start time for the first two simulations is the same:
could be this one the problem for my system? <SPAN
class=515392109-25012011>However, I did use tpbconv each time to make restarts
of my simulations, I really don't know why the start time is 0.000 in the first
two cases. </SPAN></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011>Is there a problem
in the results of simulations if these two simulations have the same start time?
<SPAN class=515392109-25012011><SPAN
class=515392109-25012011></SPAN>Practically, what can I do to concatenate my
.edr files? </SPAN></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011><SPAN
class=515392109-25012011></SPAN></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011><SPAN
class=515392109-25012011>Many thanks in advance and best
regards</SPAN></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011><SPAN
class=515392109-25012011>Anna Marabotti</SPAN></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011></SPAN></FONT><FONT
size=2 face=Arial><SPAN class=515392109-25012011></SPAN></FONT><FONT size=2
face=Arial><SPAN class=515392109-25012011></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=515392109-25012011></SPAN></FONT><FONT
size=2 face=Arial><SPAN
class=515392109-25012011></SPAN></FONT></SPAN></FONT><FONT size=2
face=Arial>____________________________________________________</FONT></DIV></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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