[gmx-users] segmentation fault while running eneconv

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 25 15:43:20 CET 2011

Anna Marabotti wrote:
> 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

What Gromacs version are you using?  If it is not 4.5.3, then you're probably 
running into a bug regarding double precision .edr files that was fixed some 
time ago.

> 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.

Well, your commands don't agree with the output of eneconv.  The names are 
different.  Perhaps you've confused what files you think you're using, or 
otherwise attempted to append to a file and then gave it a new name.  In any 
case, gmxcheck is your friend here.

> 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?

Presumably, yes.  As long as the .edr files have no internal corruptions (which, 
unfortunately, is quite possible if the job frequently went down), then you 
should be able to concatenate them.  That also depends on the version of Gromacs 
you're using, if you're running into the old bug.  It's always helpful to state 
right up front which version you're using when reporting a problem.


> 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 <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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