Claus Valka wrote:
Dear gromacs users,
my system comprises 16 polymer chains with 455 atoms
each. I want to calculate the dihedral distribution
for a number of dihedrals.
I want to create an index file which will contain the
global numbers (the third column of the gro
file-concecutive number of atoms) of the
atom-quadraplets, which will correspond to the
dihedrals I want to calculate.
If I use the make_ndx command I have to type 'a' and
then for each dihedral angle I have to type the names
of the atoms I'm interested in (for example C1 C2 C3
C4, which are four carbon atoms in my case).
If I have already created a text file which has in
every row the names of the atoms I'm interested in,
which will be the command that will give me as output
the index file I want? I suppose that I should type
only one command.
You're on the right track, see
http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive
For example the command :
make_ndx -f input_file.gro -o output_file.ndx <
input_text_file.txt
doesn't work.
Your file needs to have the same content as you'd type interactively...
so that means the "a" as well. Otherwise, since you haven't really told
us what you're doing in this file, we can't help you.
And will the output be in the format gromacs wants
(four atoms in a row)? I'm asking this because when I
typed one quadraplet the format of the index file
wasn't the one it should have been.
I'm not going to guess what you mean here. Tell us exactly what you did,
what it produced, what you expected, why the result didn't work.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
