On 1/08/2012 11:29 PM, juanjuan0618 wrote:
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？
Define them with unique names if they should be distinct, or don't
redefine them if they should be the same as the ones in the force field.
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?
You've probably got some bizarre line ending or non-text formatting.
Plain text, preferably with unix-style line endings, will work. dos2unix
tool may be your friend.
Mark
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.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/atomtypes-are-not-case-sensitive-tp4426581p4999917.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
