On 10/4/12 5:29 PM, Bao Kai wrote:
Hi, all,
I am still working on the molecular simulation of CO2 and H2O mixture.
The information of the molecules types and the force field model are
all defined in the a.top file.
1 [ defaults ]
2 ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
3 1 3 yes 0.5 0.5
4 [ atomtypes ]
5 ; type at.num mass charge ptype sigma epsilon
6 CO 6 12.0110 0.5888 A 0.27918 0.2398
7 OC 8 15.9994 -0.2944 A 0.30000 0.6872
8 OW 6 15.99940 -0.8476 A 0.316557 0.650194
9 HW 1 1.00800 0.4238 A 0.00000 0.00000
10 [ moleculetype ]
11 ;name nrexcl
12 CO2 3
13 [atoms]
14 ; nr type resnr residue atom cgnr charge mass
........
32 [moleculetype]
33 ; molname nrexcl
34 SOL 2
35 [atoms]
36 ; nr type resnr residue atom cgnr charge mass
...............
47 [system]
48 sparkling water
49 [molecules]
50 CO2 100
51 SOL 3000
I create on co2.gro file to put one CO2 molecule inside.
Then I used
genbox -ci co2.gro -nmol 190 -o a.gro -box 7. -p a.top
to put 190 CO2 molecules inside the box.
Then I used
genbox -cp a.gro -o b.gro -box 7 -cs -maxsol 9810 -p a.top
to put 9810 H2O molecules inside the box.
In the file a.top, the No. of the H2O was updated correctly, while the
No. of the CO2 molecules was not updated. The No. of the atoms in
.gro files are correct.
Can you please tell me the reason or how to solve it?
genbox only updates water molecules in the topology. Anything else is up to
you. Beware that a linear, 3-atom model of CO2 is probably not going to work
due to issues with linear angles, as has been discussed frequently on the list.
A more robust approach involves virtual sites.
-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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