[gmx-users] g_dist explanation

[Justin A. Lemkul]

On 4/23/12 10:59 AM, Shilpi Chaurasia wrote:
>   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
>

You can't print frames that aren't there.  If you saved frames using "nstxtcout 
= 1000" (assuming a time step of 2 fs), then you can't create frames in between. 
  You would need to do the run again, saving frames with greater frequency. 
Note that doing so will likely make your trajectory file quite a bit larger.

-Justin

-- 
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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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