Moeed wrote:
Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules (interaction energy between two hexane
molecules) I have 125 hexane molecules in my system. Please help me
figure out what the problem is.
make_ndx -f Hexane-Stack125.gro -o index.ndx
what I get from this command line is:
************************************************
Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
There are: 125 OTHER residues
There are: 0 PROTEIN residues
There are: 0 DNA residues
Analysing Other...
0 System : 2500 atoms
1 HEX : 2500 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
**********************************************************************************
1- Can you please help me understand what these mean? I just typed in
"q" and exit.
Doing this serves no purpose whatsoever. If you're keeping the default groups
that are already generated, there is no need for an index file. See the last
line on this page:
http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups
<snip>
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: readir.c, line: 1007
Fatal error:
Group Hexane not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the
'-n' option of grompp.
In that case use the '-n' option.
-------------------------------------------------------
mdp file:
title = Hexane
cpp = /lib/cpp
;define = -DFLEX_SPC ; This define statement is
completely irrelevant if you're not dealing with water.
constraints = all-bonds
integrator = steep
dt = 0.002 ; ps !
nsteps = 200
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 1000.0
emstep = 0.01
energygrps = Hexane Hexane
"Hexane" is not a group, but "HEX" is. Furthermore, you're defining the same
group twice. The purpose of energygrps is to specify subsets of your system for
energy terms to be written. If your system is comprised of only hexane, there
is only one group to specify.
<snip>
2- I have a
question here: why the first group is named [system] and the second Hex?
See the link quoted above.
<snip>
I though maybe I should change the name in brackets. I renamed [system]
an d{HEX}to {Hexane] . I grompped again:
Don't. If you're naming multiple groups the same thing, then you've badly
broken the purpose of an index file. From what I can see, you do not need to be
using energygrps or index files at all!
<snip>
Fatal error:
Atom 1 in multiple Energy Mon. groups (1 and 2)
If the groups are redundant, then this makes sense.
-Justin
--
========================================
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
