[gmx-users] segmentation fault while running eneconv

[Anna Marabotti]

Dear all,
 
I launched on my system a first simulation of 5 ns, then I prolonged it to
50 ns using 
tpbconv -s tpr1_5ns.tpr -until 50000 -o tpr2_50ns.tpr
and then 
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, every time I relaunched
it simply doing:
mdrun -s tpr2_50ns.tpr -cpi md2_50ns.cpt -deffnm md2_50ns_2/3/4
 
At the end of these simulations I obtained the following files:
- md1_5ns.xtc and .edr: files obtained from the first MD of 5 ns long
- md2_50ns.xtc and .edr: files obtained by prolonging the first MD until
50ns
- md2_50ns_2.xtc and .edr: files obtained by restarting the previous
dynamics that was interrupted before 50 ns
- md2_50ns_3.xtc and .edr: same as before
- md2_50ns_4.xtc and .edr: same as before
 
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:
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
and all worked fine: I obtained the output file with no errors (there are no
errors also in the .log files)
 
On the contrary, when I tried to do the same with eneconv:
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
I obtained the following output:
 
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
Reading energy frame      1 time  100.000
Opened 2GH9openmod4_pH10_50ns.edr as double precision energy file
Reading energy frame      0 time    0.000
Opened 2GH9openmod4_pH10_50ns_2.part0002.edr as double precision energy file
Reading energy frame      0 time 14900.000
Opened 2GH9openmod4_pH10_50ns_3.part0003.edr as double precision energy file
Reading energy frame      0 time 27800.000
Opened 2GH9openmod4_pH10_50ns_4.part0004.edr as double precision energy file
Reading energy frame      0 time 38800.000
 
Summary of files and start times used:
 
          File                Start time
-----------------------------------------
2GH9openmod4_pH10_5ns.edr        0.000
2GH9openmod4_pH10_50ns.edr        0.000
2GH9openmod4_pH10_50ns_2.part0002.edr    14900.000
2GH9openmod4_pH10_50ns_3.part0003.edr    27800.000
2GH9openmod4_pH10_50ns_4.part0004.edr    38800.000
 
Opened 2GH9openmod4_pH10_5ns.edr as double precision energy file
Segmentation fault

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:
http://lists.gromacs.org/pipermail/gmx-users/2007-January/025657.html
 
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?
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. 
Is there a problem in the results of simulations if these two simulations
have the same start time? Practically, what can I do to concatenate my .edr
files? 
 
Many thanks in advance and best regards
Anna Marabotti
 
____________________________________________________
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
man"
 
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