[gmx-users] g_dist explanation

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Mon Apr 23 17:27:00 CEST 2012

Use trjconv -skip first for your trajcetory so you can rewrite it every frame/time step you want. Then proceed to g_dist.


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Shilpi Chaurasia [shilpi.chaurasia at unimi.it]
Sent: Monday, April 23, 2012 3:59 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] g_dist explanation

 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120423/966b154c/attachment.html>

More information about the gromacs.org_gmx-users mailing list