Алексей Раевский wrote:
mm...sorry for incorrect explanation of the task. I know how to use
index_ndx and g_select, but I don't know whether it is possible to
create an index group of all atoms in !!sphere!! with a radius of 10
angstrom around selected "carbon" (for example). Exactly I don't know
In this case, no, probably not. You can get individual spheres of water around
each carbon, which may roughly come out to what you want.
how and where to determine a sphere's parameters. As you understand if
this sphere includes SOL molecules (which are flexible and all time will
be changing one to another from outside to the inside of the sphere), so
I have to define not atom numbers of SOL but constant spatial character
of the sphere. IS IT possible? With a use of index file it will look
like a new index.ndx, with [sphere] section and its content, for each frame
You can only generate snapshots. You're right, since molecules move, the
indices are dynamic. If you tried to get a whole trajectory with your criteria,
almost certainly some frames would have different numbers of atoms. Gromacs
currently does not support this.
-Justin
------------------------------
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Date: Sat, 10 Sep 2011 00:00:23 +0300
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Hi. I've look through the manual and didn't find an answer on my
question:
i've got a trajectory and i want to convert it in *.pdb with such
parameters
of index file [all atoms within a sphere with a chosen radius around
selected atom]. What can i do? Thank you
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Nemo me impune lacessit*
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Message: 5
Date: Fri, 09 Sep 2011 17:02:40 -0400
From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] (no subject)
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Алексей Раевский wrote:
> Hi. I've look through the manual and didn't find an answer on my
> question: i've got a trajectory and i want to convert it in *.pdb
with
> such parameters of index file [all atoms within a sphere with a
chosen
> radius around selected atom]. What can i do? Thank you
>
Use g_select to generate the index group and trjconv to write the
file in the
format (and with the contents) that you want.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
/С уважением!
///
/
Nemo me impune lacessit/
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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