jojo J wrote:
Hello,
I am trying to make two different groups from residues below. one under
the name Solute (residues a and b) and the other for solvent (residue c,
SOL). The only way I know now is to do this by splitting the list of
atom numbers [system] (default index file), from 1 to 362 and creating a
new directive [SOL] and putting the rest of the atoms under this
directory. Can you please help how to do this using the commands like
nr, name... I could not do that by reading the help option Thanks
Each [moleculetype] should be its own default group, i.e.:
http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups
Making selections from these is trivial. Unless you've got some bizarre
topology organization such that you only have a [System] group, then it should
be very easy to merge groups as necessary. For instance, if A and B are
different moleculetypes, merging them can be done with:
A | B
If you need to merge based on subsets of groups and you know the residue
numbers, you can apply the same concept:
r 1 | r 2
Solvent (SOL) should already be a default group, so I'm not seeing why you have
to create it yourself.
-Justin
0 System : 20343 atoms
1 a : 10 atoms
2 b : 333 atoms
3 c : 20000 atoms
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.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
