Dear professor,
Now I want to simulate the water and carbon dioxide mixture solution,but
when I do the simulation with my own .gro and .itp files, I met some
questions.
I use gromacs4.0.7 and the water model is TIP4P2005.
Q1: when I grompp the .gro( a CO2 molecular and 1240 water moleculars), .top
and .mdp files, it prompts me
WARNING 1 [file co2.itp, line 3]:
Overriding atomtype C
WARNING 2 [file co2.itp, line 4]:
Overriding atomtype O
how can I remove these warning？
Q2： when I grompp the other .gro with a water cage(20 water moleculars)
containing a CO2 molecular and 1240 water moleculars， it prompts me
Syntax error - File co2.itp, line 1
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
Can you tell me how I could remove this error?
my co2.itp is following:
[ atomtypes ]
; type mass charge ptype sigma epsilon
C 12.01100 0.5888 A 0.27918 0.239832
O 15.99940 -0.2944 A 0.30000 0.687244
[ moleculetype ]
; molname nrexcl
CO2 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 C 1 CO2 C 1 0.5888
2 O 1 CO2 OC1 1 -0.2944
3 O 1 CO2 OC2 1 -0.2944
#ifdef FLEXIBLE
[ bonds ]
; i j funct length force.c.
1 2 1 0.1163 345000.0 0.1163 345000.0
1 3 1 0.1163 345000.0 0.1163 345000.0
[ angles ]
; i j k funct angle force.c.
2 1 3 1 180.00 383 180.00 383
#else
[ settles ]
; C funct dco doo
1 1 0.1163 0.2326
[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
Looking forward to your reply, thank you very much.
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