Gavin Melaugh wrote:
Hi Justin
I Did the following and it worked. You were right about using one atom
types directive. If you don't mind I have another query. In all my
topology files to date (one molecule type), I have always listed the
atomtypes in the [atomtypes] directive, and used the set up in
[defaults] below. Is this all that is required for the calculation of
the LJ energies. I have never used a pair list, a pair types directive
or a nonbond_params directive. From the output I still get LJ energies
but I am slightly confused by all the different options.
I can't give a better explanation than what is already in the manual,
specifically section 5.3.3 ([nonbond_params] and whether or not you need it).
Whether or not you need [pairs] depends on the underlying mechanics of the force
field you're using. See section 5.3.5.
-Justin
parameter level
[defaults]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
[atomtypes]
;type mass charge ptype sigma(nm)
epsilon(kjmol-1)
CB 12.011000 0.000000 A 0.355000 0.292880
CA 12.011000 -0.115000 A 0.355000 0.292880
HC 1.008000 0.115000 A 0.242000 0.125520
CU 13.019000 0.265000 A 0.350000 0.334720
NU 14.007000 -0.597000 A 0.325000 0.711280
CH 13.019000 0.332000 A 0.385000 0.334720
C3 15.035000 0.000000 A 0.390500 0.732200
CT 12.011000 -0.180000 A 0.350000 0.276144
HH 1.008000 0.060000 A 0.250000 0.125520
#include "tertpentane.itp"
#include "methylcage.itp"
;System level
[system]
;the name of this system
cage and pentane
[molecules]
; moleculename number
tertpentane 1
methylcage 1
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Justin
Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?
You only need to use an [atomtypes] directive if you're introducing
new atom types into the force field. I don't know if it's necessary.
I also don't know if these sections can be discontinuous (i.e., one
section present in cage.itp, another in tertpentane.itp). Try the
approach I sent you and see. If you get fatal errors, then you may
have to assemble a single [atomtypes] directive and put it either in
the first .itp file you #include, or before any of the #includes in
the .top (since #include really just means "cut-and-paste the stuff
here," it works the same).
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi Mark.
I have looked this up, but I am a little uncertain. Does one of the
topologies have to be included within the other as an .itp file. If so
No. You #include .itp files to simply add molecules within a .top; it
would be very rare to #include an .itp within an .itp (although it can
be done). For your case, your .top is simple:
#include (force field)
#include "cage.itp"
#include "pentane.itp"
[ system ]
My system
[ molecules ]
Cage 1
Pentane 1
do I only define the [defaults directive] in the .top file i.e. I take
it I don't include this directive in the .itp file as well.
The [defaults] directive is provided by whatever force field you
#include. If you're using some custom parameters, then it needs to be
defined once (and only once) at the top of your .top file. Otherwise,
you'll get fatal errors from grompp.
-Justin
Cheers
Gavin
Mark Abraham wrote:
Look up the include file mechanism on the webpage.
Mark
----- Original Message -----
From: Gavin Melaugh <gmelaug...@qub.ac.uk>
Date: Tuesday, September 28, 2010 19:04
Subject: [gmx-users] topology file for two molecules
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Hi all
I want to run a simulation of one tert-pentane molecule inside one
organic cage molecule. I have the topology files for both
molecules but
obviously I only need one .top file as the input for grompp.
What is the
most convenient way of having both topologies in one file?
Many Thanks
Gavin
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--
========================================
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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