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.
-Justin
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.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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
