[gmx-users] Velocity as a function of distance Z

Kamps, M. m.kamps at student.rug.nl
Fri Mar 3 11:49:48 CET 2017

(previous mail was sent prematurely, my apologies)

Dear Mark,

Again, thanks for the reply.

You said I should identify groups of molecules that are to my
interest. I'm unsure how to do this.
My .gro files show no distinction between different molecules, all of
them are built the same (rows deleted for clarification).

    1EthB    C1 5963  18.910   0.037   2.874  0.4243  0.6722 -0.0361
    1EthB   H11 5964  18.969   0.099   2.810  1.4488  0.2545  0.0251
    5Eth    H21 5992  18.287   0.495   3.423  0.1969  0.2998  0.4129
    5Eth    H22 5993  18.291   0.508   3.251  0.7485 -2.7065  0.0733
   10EthE   H22 6023  17.188   0.735   3.427 -0.4008 -2.3617  0.5620
   10EthE   H23 6024  17.153   0.699   3.263  2.2014  0.6628 -1.8300

What should I enter to select individual molecules? There are no
columns or names that are unique to a single molecule?
In the 'Selection syntax and usage' document there are tons of
options, however I find it difficult to know which one to use, and how
to use them.
The distinctions that I can make are in their residue
(EthB-(Eth)n-EthE), which will select all atoms in these groups,
instead of whole molecules. I could also make a selection based on
their position, however that would mean not entire molecules are
taken. When i say for example resname EthB EthE Eth and x>5 and x<7,
all atoms inside this margin will be taken, however this would mean it
will select partial/split/cut molecules, since parts of the molecule
will be outside of this frame. When looking at the earlier mentioned
document, I see for example the 'chain' option. But I can't figure out
how to use this.

My residue groups are defined via residuetypes.dat to be:
Eth    Polymer
EthB    Polymer
EthE    Polymer
While in my topology they are called simply:
Is this helpful to make a molecule selection?


>>> 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
>>> traj?
>> 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
>> first.
>> Mark
>>> I'm getting lost in all the options, any help would be appreciated.
>>> Mark

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