[EMAIL PROTECTED] wrote:
[EMAIL PROTECTED] wrote:
Hi gromacs users,
I worked a on my problem (see mail below) and got some new questions:
I did REMD using 50 replicas using gromacs version 3.3, while the data
were saved every 20 ps and exchanges were attempted every 5 ps. I used
demux.pl to generate replica_temp.xvg and replica_index.xvg. To get
continuous trajectories I used trjcat from version 3.3.1 (it's not
available in older versions)
trjcat -f traj*.xtc -demux replica_index.xvg
I solved the segmentation fault problem by compiling gromacs 3.3.1
differently. But now I'm stuck with the same problem as other people
before. trjcat produces only one output file trajout.xtc which contains
only the box parameters and looks like this:
trajout.xtc frame 0:
natoms= 0 step= 0 time= 0 prec= 0
box (3x3):
box[ 0]={ 5.46920e+00, 0.00000e+00, 0.00000e+00}
box[ 1]={ 1.82296e+00, 5.15645e+00, 0.00000e+00}
box[ 2]={-1.82292e+00, 2.57794e+00, 4.46567e+00}
not available: x
trajout.xtc frame 1:
natoms= 0 step= 5000 time= 20 prec= 0
box (3x3):
box[ 0]={ 5.46920e+00, 0.00000e+00, 0.00000e+00}
box[ 1]={ 1.82296e+00, 5.15645e+00, 0.00000e+00}
box[ 2]={-1.82292e+00, 2.57794e+00, 4.46567e+00}
not available: x
trajout.xtc frame 2:
.... and so on.
Is the problem caused by the different time frames in the traj*.xtc
files
and the replica_index.xvg file? Or is it caused by mixing up the
different
gromacs versions? For other people using the demux.pl script seemed to
solve all the problems but it does not in my case.
Thanks for your help.
Cheers, Madeleine
did you read the help text in the perl script?
Yes, I did.
# If your exchange was every N ps and you saved every M ps you can make
for
# the missing frames by setting extra to (N/M - 1). If N/M is not integer,
# you're out of luck and you will not be able to demux your trajectories
at all.
In my case N=5 ps and M=20 ps which means (N/M-1) is not an integer and I
m unlucky. But I only need to know every 20 ps at which temperature each
replica is simulated. Even if I produce a replica_index file that contains
only the information each 20 ps, trjcat produces one trajout.xtc file
which contains only the box parameter as posted above.
I would think it is reverse N=20 M = 5, so you have to set the number to
3. You can test it by computing RMSD for the resulting trajectories and
seeing whether these are continuous.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
---
Madeleine Kittner, PhD student
Department of Theory and Bio-Systems
Max Planck Institute of Colloids and Interfaces
Research Campus Golm
14424 Potsdam, Germany
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
_______________________________________________
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