On 5/5/12 10:21 PM, Za Pour wrote:
Dear Justin
I appreciate for your reply.I used -maxwarn option because grompp gave me:
WARNING 1 [file ffbonded.itp, line 2705]:
Overriding Bond parameters.
old: 0.151 292880 0.151 292880
new: C C 1 0.1418 478900
OK, that's reasonable.
I guess I am not using improper in the topology file.my cnt.top file looks like:
; Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
CNT 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 opls_995 1 UNK C 1 0 12.011 ; qtot 0
2 opls_995 1 UNK C 2 0 12.011 ; qtot 0
3 opls_996 1 UNK C 3 0 12.011 ; qtot 0
......
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 1.420000e-01 4.789000e+05 1.420000e-01 4.789000e+05
1 73 1 1.420000e-01 4.789000e+05 1.420000e-01 4.789000e+05
2 4 1 1.420000e-01 4.789000e+05 1.420000e-01 4.789000e+05
.....
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 3 1
1 5 1
1 71 1
......
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 73 1 1.180000e+02 5.622000e+02 1.180000e+02 5.622000e+02
1 2 4 1 1.190000e+02 5.622000e+02 1.190000e+02 5.622000e+02
4 3 9 1 1.200000e+02 5.622000e+02 1.200000e+02 5.622000e+02
........
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
73 1 2 4 3 1.910000e+02 5.000000e+00 3.000000e+00 1.910000e+02 5.000000e+00
3.000000e+00
2 1 73 72 3 2.520000e+02 5.000000e+00 3.000000e+00 2.520000e+02 5.000000e+00
3.000000e+00
1 2 4 3 3 2.240000e+02 5.000000e+00 3.000000e+00 2.240000e+02 5.000000e+00
3.000000e+00
........
I'm only guessing about the impropers, but if you don't have any, then the
carbon rings will deform, which I'm also guessing is part of your problem.
There is a tutorial linked from
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube that may be useful.
It also does not appear to use any defined impropers, but perhaps its workflow
and information will yield better results.
-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
