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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
