On 8/4/12 10:31 AM, juanjuan0618 wrote:
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.
Thank you very much for your answers, Question 1 has been solved, but the
second question is still appearing. I try to change the file style to unix
by using dos2unix, but the problem isn't solved.
When I change the order of the including file of the topology file, it may
prompts me
Syntax error - File tip4p.itp, line 4
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype
or prommpt me
Syntax error - File co2.itp, line 1
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
I can't find what's error, and I don't know how to solve the
problem. Can you tell me what could I to remove this error?
http://gromacs.5086.n6.nabble.com/file/n4999956/co2.itp co2.itp
http://gromacs.5086.n6.nabble.com/file/n4999956/co2-01-00.top co2-01-00.top
Looking forward to your reply, thank you very much.
There is an order in which directives are allowed to appear. Refer to Chapter 5
of the manual. All directives at the force field level ([defaults],
[atomtypes], etc) must come before any [moleculetype] can be declared. If
you're moving around #include statements, you're probably breaking the required
order.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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