Re: [gmx-users] keep the nanotube cylindrical.
On Sat, May 5, 2012 at 7:27 PM, Za Pour za.p...@yahoo.com wrote: Dear gmx users I am simulation a system including carbon nanotube+water.I have done these things: 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. Best regards I had a similar issue, but I modeled the CNT carbon atoms as opls_147, trying not to change the parameters too much, so I kept the bond lengths, angles and force constants untouched. I noticed that removing the [ dihedrals ] section from the resulting topology significantly reduced the tube deformation. Since g_x2top doesn't generate impropers and a CNT has no rotable bonds, these dihedrals are spurious, anyway. Also, do your tubes have open ends? If you can afford to have periodic tubes, so that the box z length is a multiple of the tube unit cell and the tube ends are bonded through the box wall, it seems much more stable. Or you could try capped tubes. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] keep the nanotube cylindrical.
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 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 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. Best regards-- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] keep the nanotube cylindrical.
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
