[gmx-users] Velocity as a function of distance Z (Mark Abraham)

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 3 08:28:17 CET 2017


On Wed, 1 Mar 2017 14:11 Kamps, M. <m.kamps at student.rug.nl> wrote:

Dear Mark,

Thanks again for your reply. I'm sorry for asking these probably
stupid questions, but I'm not able to figure it out.

The objects I am interested in are small polymers, consisting of three
residue groups; Eth EthE and EthB (corresponding to both the end
groups of a polymer, and the middle section). I total these groups
consist of around 25000 atoms.

Those names won't help you. You want to identify (groups of) single
molecules. Look at your file and see what distinguishes them.

With gmx select I will enter the following command, at an arbitrarily
chosen time:
gmx select -f input.trr -s input.tpr -on output.ndx -b 7.5 -e 7.5
In the following selection screen my preferred molecules are listed as
three different groups (Eth, EthE and EthB), therefore I manually
select these groups with the command: resname Eth EthE EthB, press
enter and end with Ctrl-D. It will then proceed to process the frames,
where GROMACS tells me it has analyzed 1 frame, at the 30th timestep,
which is 7.5.

I can't see everything, but probably all you did was select every atom,
which won't help you. You wanted all the molecules with some criterion, so
you will need to make a better selection.

I will then switch to gmx traj where I enter the following:
gmx traj -f input.trr -s input.tpr -n output.ndx -ov output.xvg
It will then process all frames, and not only the frame I selected
during gmx select. Do I need to specify -b and -e again during gmx

Yes, once you've made a selection that matches geometric criteria from a
frame, it is literally only applicable to that frame.

Then, the output could be read with xmgrace, however looking at the
files it will try to plot 25000 different lines, which it probably
cant. Opening the .xvg file plots the velocity/time plot of only 1
atom, while opening the  .xvg file for the time selected output (via
gmx traj -b -e) shows an empty plot for only one atom.

You haven't selected eg one molecule from one frame yet, so get that right


I'm getting lost in all the options, any help would be appreciated.

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