Elisabeth wrote:
Hello to all,
I am looking for bonded and nonbonded parameters for C H atoms in
saturated hydrocarbons.
atom types are:
Carbon atoms opls_135 opls_136
H opls_140
opls_135 12.01100 ; alkane CH3
opls_136 12.01100 ; alkane CH2
opls_140 1.00800 ; alkane H.
Please help me out with the following:
- I am wondering if I am selecting the correct values, for C-C and C-H
bonds from ffoplsaabon.itp.
The C-C bond is not correct for alkanes. It is for the C-C bond of oxalic acid,
as the comment indicates. In ffnonbonded.itp, you can see how opls_* types are
mapped to different bonded atom types (for instance, opls_135/136 are CT). Note
that in the topology, you do not have to explicitly define values when using
OPLS-AA; any bond between two defined bonded atom types will be automatically
detected and used.
C C 1 0.15100 292880.0 ; wlj oxalic acid, etc.
HC C 1 0.10900 284512.0 ; wlj 7/96
- what does wlj mean?
Probably someone's initials, which occur frequently to indicate either the
source of the parameters or the individual that added them. In this case, my
guess would be Jorgensen is the referenced individual here.
- what are the units?
This is in the manual.
Angle
CA CA CZ 1 120.000 585.760 ; wlj
CA CA CR 1 120.000 527.184 ;
CA CA CX 1 120.000 711.280 ;
C CT Cl 1 109.800 577.392 ; wlj
- I can not distinguish CA CZ .... What are they referring to?
See the above tip about converting atom types in ffnonbonded.itp.
[ dihedraltypes ]
C C CT HC 3 0.17782 0.53346 0.00000
-0.71128 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000)
- Is this what I need for oplsaa 135 136 140?
Probably not. The comment indicates the dihedral is for dicarbonyls. The
appropriate dihedral is:
CT CT CT HC 3 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000 ; hydrocarbon all-atom
Note how the comment indicates it is for use with hydrocarbons. Again, like
bonds as described above, you do not need to explicitly list parameters in the
topology. They will be inferred from the atom types.
ffoplsaanb.itp.
opls_135 CT 6 12.01100 -0.180 A 3.50000e-01
2.76144e-01
opls_136 CT 6 12.01100 -0.120 A 3.50000e-01
2.76144e-01
opls_140 HC 1 1.00800 0.060 A 2.50000e-01
1.25520e-01
- are these parameters for
opls_135 12.01100 ; alkane CH3
opls_136 12.01100 ; alkane CH2
opls_140 1.00800 ; alkane H.
?
Yes.
Also in usr/local/gromacs/share/gromacs/top/ directory I can not find
ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in previous
versions these files were accessible. I am using itp files from version
4.0.7 and wanted to make sure the above parameters for oplsa_135
oplsa_136 and oplsa_140 have been remained unchanged in 4.5.4. Where can
I find these files?
The force field organization has changed, but the content of the force fields
has not. This is described in the manual. All the equivalent files are now in
the oplsaa.ff subdirectory. For backwards compatibility, the statement #include
"ffoplsaa.itp" will indeed call the force field, because you will note that
ffoplsaa.itp now simply calls the correct force field with #include
"oplsaa.ff/forcefield.itp."
-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
========================================
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