[gmx-users] The No. of the CO2 melecules in top file can not be updated correctly
paeanball at gmail.com
Fri Oct 5 11:18:45 CEST 2012
Thank you for your reply.
It is a little weird and inconvienient that genbox does not update the No.
of solute molecules. Is it designed in this way? Does it have any reason
For my case, the inear, 3-atom model of CO2 works pretty well. I got the
model from a paper from Zhenhao Duan. I guess I will use this model for
the project before I get something wrong.
> Message: 5
> Date: Thu, 04 Oct 2012 17:34:22 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] The No. of the CO2 melecules in top file can
> not be updated correctly.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <506E00DE.9050505 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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
> > 6 CO 6 12.0110 0.5888 A 0.27918
> > 7 OC 8 15.9994 -0.2944 A 0.30000
> > 8 OW 6 15.99940 -0.8476 A 0.316557
> > 9 HW 1 1.00800 0.4238 A 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
> you. Beware that a linear, 3-atom model of CO2 is probably not going to
> due to issues with linear angles, as has been discussed frequently on the
> A more robust approach involves virtual sites.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users