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

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 3 14:47:09 CET 2017

On Fri, Mar 3, 2017 at 11:50 AM Kamps, M. <m.kamps at student.rug.nl> wrote:

> (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?

Here, residue numbers 1-10 look like a molecule. If so, then residue 11-20
might be a second one, etc. So you can set up some groups via something like
molecule1 = resindex 1 to 10;
molecule2 = resindex 11 to 20;
etc. Perhaps needing a script to generate that, to re-use a bunch of times.
Perhaps, if given a .tpr, we could extend the selection syntax to be aware
of molecules.

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.

First, make sure you can write a sentence that completely describes how you
want to select things, e.g. from the frame at time x I want a set of index
groups, with each group a single molecule, whose center of mass has a z
coordinate between n and m. Then work out how to express that, e.g by
starting to work out how to select a single molecule based on
Just guessing at syntax doesn't help you work out what you actually want :-)

> 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.

So maybe

molecule1 and com of molecule1 (z > 11 or z < 13)

I'm no expert on the selection syntax, since I've never used it to solve a
serious problem, so do start a new thread if you can't find something that


My residue groups are defined via residuetypes.dat to be:
> Eth    Polymer
> EthB    Polymer
> EthE    Polymer
> While in my topology they are called simply:
> C20H42
> C16H34
> Is this helpful to make a molecule selection?
> Mark

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