[gmx-users] water molecules (interfacial)

Teemu Murtola teemu.murtola at cbr.su.se
Sun Nov 14 19:44:06 CET 2010

On Sun, Nov 14, 2010 at 14:50, leila karami <karami.leila1 at gmail.com> wrote:
> I made a selection.dat file as follows:
> waterO = group SOL and name OW;
> heavy1 = group Protein_A and group "Protein-H";
> heavy2 = group Protein_B and group "Protein-H";
> inter = waterO and within 0.35 of heavy1 and within 0.35 of heavy2;
> is my selection.dat file true?

Your selection.dat only specifies several variables, but never uses
any of these; this is the reason why you get the message "Nothing
selected".  Variable definitions (any lines with an assignment) are
only meant as convenient notation and/or for optimization, and do not
define selections as such.  It appears that what you want to do is
accomplished by adding a line "inter;" at the end of the file, or
removing "inter =" from the last line.  Please take a look at the
examples accessible through -select "help examples".

> when I used g_select -f .xtc -s .tpr -n .ndx -os -oc -oi -om -on -sf
> selection.dat -select, what should be put in front of -select to avoid
> Nothing selected, finishing up?

You should not use -sf and -select at the same time; at most one of
them gets used at a time, as explained in the online help (-select
"help cmdline").  It may be that the help is not exactly accurate if
you pass an empty string to -select, but nevertheless, these options
have not been designed to be used simultaneously.


PS. Please don't send e-mail to me personally.  All such questions are
better asked on the gmx-users list, where someone else may also be
able to help you as well.  Also, in this case, the question you sent
to the list ~1 hour after the personal e-mail was in fact much more to
the point.  Without the information contained in the latter, you
probably would not have gotten a useful reply.

PPS. I'm no longer employed in the academia, so please don't expect an
immediate reply.  You may cc me on an e-mail to the list if you
haven't gotten any reply on the list, and I'll try to take a look when
I have sufficient free time.

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