[gmx-users] Velocity as a function of distance Z
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
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.
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:
> Is this helpful to make a molecule selection?
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