Dear Gromacs users,
i am adding new residue to the existing charmm27
force field of the gromacs and i am planning to use buckingham potential
for the non bonded interactions. for that i made following changes to the
ffnonbonded.itp file
[ atomtypes ]
;name at.num mass charge ptype sigma epsilon
CC32A 6 12.01100 0.1030 A 0.0
0.0 0.0
HCA2 1 1.00800 0.0355 A 0.0
0.0 0.0
OC30A 8 15.999400 -0.3480 A 0.0
0.0 0.0
[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4
INTERACTIONS
OC30A OC30A 1 0.0 0.0
OC30A CC32A 1 0.0 0.0
OC30A HCA2 1 0.0 0.0
CC32A CC32A 1 0.0 0.0
CC32A HCA2 1 0.0 0.0
HCA2 HCA2 1 0.0 0.0
;########### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6)
[ nonbond_params ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4
INTERACTIONS
OC30A OC30A 2 243922.5976 40.2414486921 0.000803746
OC30A CC32A 2 179625.8144 36.297640653 0.001476115
OC30A HCA2 2 85489.9984 40.899795501 0.000413379
CC32A CC32A 2 132277.5784 33.05785124 0.002710395
CC32A HCA2 2 62955.3928 36.832412523 0.000759396
HCA2 HCA2 2 29962.4608 41.58004158 0.000212547
;########### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6)
;D = A, B = 1/P, C = E
and in the default directive of the forcefield.itp i made the following
changes
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
2 1 no 0.0 0.0
what values should i give for the sigma and epsilon in the [ atomtype ]
directive and pairtypes directive . if i ignore the pair types it giving
error no default Lj 1-4 interactions. though i am using nbfun as 2 to use
the buckingham potential. I have only the values of the A,B,C. How to get
sigma and epsilon if they are required.
Did i modify the ffnonbonded.itp in the correct manner ? or any thing went
wrong?
please help me in this regard.
Thank you in advance.
Regards,
Ramesh.
--
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
