?Hi Gromacs users,
I am using pull code to separate two units of a protein dimer. I have run the
pulling simulation for 650 ps and got pullx.xvg and pullf.xvg files, where the data
is printed at every 0.01 ps (according to pull_nstxout& pull_nstfout, both are
10 in this case) as given below
0.0000? 0.000322052
0.0100? 0.173534
0.0200? 0.297454
0.0300? 0.416585
0.0400? 0.519195
0.0500? 0.597541
...
Now, I want to calculate the distance between COM of two groups using g_dist
and printing the output data in the same time steps as in .xvg files. I tried
but the output data is printed at every 2ps steps as following:
?? 0.0000000??? 8.0175037?? -0.0010343?? -0.0055513??? 8.0175018
?? 2.0000000??? 8.0188007?? -0.0202498?? -0.0114326??? 8.0187674
?? 4.0000000??? 8.0377693?? -0.0229554?? -0.0129814??? 8.0377254
?? 6.0000000??? 8.0435743?? -0.0226321?? -0.0043244??? 8.0435410
?? 8.0000000??? 8.0615864?? -0.0312104?? -0.0116682??? 8.0615177
...
command used
g_dist -f? *.xtc -s *.tpr -n index.ndx -o dist.xvg -b 0 -dt 1 -e 650
I have also tried by using different values for 'dt' but it doesn't help.
If someone could tell me how to control the time steps in g_dist output, in
this case I want the output to be printed in the steps of 0.01 ps
thanks,
Shilpi
pull_nstxout and pull_nstfout are only relevant for pullx.xvg and pullx.xvg.
To control the output in *.trr and *.xtc (and therefore for g_dist and
most other analysis tools) you need to adjust:
nstxout (for *.trr)
nstxtcout (for *.xtc)
Greetings
Thomas
--
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
