[gmx-users] keep the nanotube cylindrical.

[Justin A. Lemkul]

On 5/5/12 1:27 PM, Za Pour wrote:
> Dear gmx users
> I am simulation a system including carbon nanotube+water.I have done these things:
> 1. I copied oplsaa.ff folder in my working directory
> 2. I added following lines to atomname2type.n2t
> C opls_995 0 12.011 2 C 0.142 C 0.142
> C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
> C opls_997 0 12.011 1 C 0.142
> 3.I added these to ffbonded.itp
> [ bondtypes ]
> C C 1 0.1418 478900
>
> [ angletypes ]
> C C C 1 120.000 562.2
>
> [ dihedraltypes ]
> C C 1 0.000 167.360 1
> 4.I added these to ffnonbonded.itp
> opls_995 C 6 12.01100 0.000 A 3.85100e-01 4.39600e-01
> opls_996 C 6 12.01100 0.000 A 3.85100e-01 4.39600e-01
> opls_997 C 6 12.01100 0.000 A 3.85100e-01 4.39600e-01
> 5.then I run g_x2top with this command:
> g_x2top -f cnt.pdb -o cnt.top -name CNT -nexcl 3 -kb 478900 -kt 562.2
> 6.then I used editconf and genbox:
> editconf -f cnt.pdb -o cnt.gro -d 1 -bt cubic
> genbox -cp cnt.gro -cs spc216.gro -o sol.gro -p cnt.top
> 7.I run grompp for EM with this command:
> grompp -f em.mdp -c sol.gro -p cnt.top -o em.tpr -maxwarn 1

Why is -maxwarn necessary here?

> mdrun -deffnm em
> 8.again I run grompp for equilibration phase:
> grompp -f nvt.mdp -c em.gro -p cnt.top -o nvt.tpr -n index.ndx -maxwarn 1

Same question here.

> mdrun -deffnm nvt
> However as I looked into the nvt.gro I realized that the cylindrical shape of
> carbon nanotube
> has been changed.I am not sure what I have done is correct or not?and how to
> keep nanotube cylindrical ? any help would be really appreciated.

Are you using impropers in the topology?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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