SV: SV: SV: SV: [gmx-users] g_saltbr

[Sarah Witzke]

Sarah Witzke wrote:

<snip>

> In each of the files are a set of distances as a function of time - it does not seem that strange, that the size is equal then.
>
> When I plot for instance the four .xvg files mentioned above I get four different curves. Also "diff" lists that every line is different.
>
> I really don't understand what I'am doing wrong.
>

    I don't know that you are necessarily doing anything wrong, but it's hard to
   diagnose the potential problems without actually seeing what might be in those
   .xvg files.  Can you post short snippets of a few of them, just to demonstrate
   what the difference is?  I am wondering if there is so much memory required,
   that the calculation is dumping out the resulting data prematurely and therefore
   over-writing incomplete output files.  Just a guess, but worth considering.


Before I got to answer this email, Tsjerk posted what I think is the answer. Here is though four files with the same name except the #s. They are only for the last 10 ns with -dt 1000 to shorten them:


::::::::::::::
sb-DMPC191:DMPC192.xvg
::::::::::::::
# This file was created Wed Dec  2 00:56:33 2009
# by the following command:
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc
-s dmpcdpac32na32-1.tpr -b 210000 -dt 1000 -sep
#
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S:
#
# Good gRace! Old Maple Actually Chews Slate
#
@    title "sb-DMPC191:DMPC192.xvg"
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@TYPE xy
    210000     3.54172
    211000     3.63549
    212000     3.82094
    213000     3.87692
    214000     3.72715
    215000     3.69254
    216000     3.76674
    217000      3.5567
    218000      3.4372
    219000     3.49882
    220000     3.35077
::::::::::::::
#sb-DMPC191:DMPC192.xvg.1#
::::::::::::::
# This file was created Wed Dec  2 00:56:33 2009
# by the following command:
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc
-s dmpcdpac32na32-1.tpr -b 210000 -dt 1000 -sep
#
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S:
#
# Good gRace! Old Maple Actually Chews Slate
#
@    title "sb-DMPC191:DMPC192.xvg"
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@TYPE xy
    210000     2.96721
    211000     3.69049
    212000     3.77841
    213000     3.28861
    214000     3.10005
    215000     2.96617
    216000     3.12796
    217000     3.48478
    218000     3.62286
    219000     3.64729
    220000     3.42346
::::::::::::::
#sb-DMPC191:DMPC192.xvg.2#
::::::::::::::
# This file was created Wed Dec  2 00:56:33 2009
# by the following command:
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc
-s dmpcdpac32na32-1.tpr -b 210000 -dt 1000 -sep
#
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S:
#
# Good gRace! Old Maple Actually Chews Slate
#
@    title "sb-DMPC191:DMPC192.xvg"
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@TYPE xy
    210000     3.34607
    211000     3.72107
    212000     3.73002
    213000     3.57064
    214000     3.42572
    215000     3.34358
    216000     3.45839
    217000     3.41128
    218000     3.91261
    219000     3.99654
    220000     3.77672
::::::::::::::
#sb-DMPC191:DMPC192.xvg.3#
::::::::::::::
# This file was created Wed Dec  2 00:56:33 2009
# by the following command:
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr -f dmpcdpac32na32-all.xtc
-s dmpcdpac32na32-1.tpr -b 210000 -dt 1000 -sep
#
# /home/nat-mem-sw/sawit02/gromacs-4.0.4/bin/g_saltbr is part of G R O M A C S:
#
# Good gRace! Old Maple Actually Chews Slate
#
@    title "sb-DMPC191:DMPC192.xvg"
@    xaxis  label "Time (ps)"
@    yaxis  label "Distance (nm)"
@TYPE xy
    210000      3.1681
    211000     3.62663
    212000     3.85572
    213000     3.58639
    214000     3.38853
    215000     3.31324
    216000     3.43343
    217000     3.27437
    218000     3.14695
    219000     3.15015
    220000     3.00437


Thank you again for all your help!

Sarah


   -Justin

--
========================================

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

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