[gmx-users] g_dist explanation

[Thomas Schlesier]

> ?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