[gmx-users] Question about topology construction.
sujithks58 at gmail.com
Thu Mar 20 15:21:31 CET 2014
I am using gromacs-4.6.5. For the sake of practice, I made a .itp file
for carbon dioxide based on the EMP2 model (J.Phys.Chem 1995, 99,
The file is self-contained with all parameters including the [default]
I tried to do run a simulation on a system containing only CO2 molecules.
My topology file included only the .itp which I made and no other
forcefield.itp is included. (Is it ok to do so?)
When I try to generate .tpr for an energy minimization, I get the error
"Found a second defaults directive" which the manual says is due to second
defaults being set in an included topology file.
BUT, Here I am defining 'default' only once, which is in the .itp file
for CO2 which I made and no other .itp from any forcefield is included. So
I am not sure how it is the "second" default and what is causing the
error. Is it necessary that the .itp should be included in some forcefield
directory although it has all the parameters, and then include it into .top
as a subset of the forcefield?
Please let me know what you think.
Have a look at the .itp I made for CO2 and please let me know if anything
is seriously wrong.
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 no 1.0 1.0
; name mass charge ptype sigma epsilon
CA 12.01100 0.6512 A 0.2757 0.2339
CO 15.99940 -0.3256 A 0.3033 0.6695
; name nrexcl
; nr type resnr residue atom cgnr charge mass
1 CA 1 CO2 CA 1 0.6512 12.0110
2 OC 1 CO2 OC1 1 -0.3256 15.9994
3 OC 1 CO2 OC2 1 -0.3256 15.9994
; i j funct doc
1 2 1 0.1149
1 3 1 0.1149
1 2 3
2 1 3
3 1 2
; i j k funct a0 ak
1 2 3 1 180 1236
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