On 15/02/2012 5:42 PM, ramesh cheerla wrote:
Dear Gromacs users,
I am planing to use buckingham
potential for the non-bonded interactions of my system. I know that
by changing the nbfunc to 2 in [ defaults ] directive of topology will
allow to use the Buckingham potential , But I don't know how to
specify the A, B,C values in the ffnonbonded.itp file.
With [ nonbond_params], not [atomtypes] or [pairtypes]. See table 5.4 of
section 5.7.1 of manual.
Mark
what values should I specify in the [ atomtypes ] directive . As i
know only A,B,C values for the pairs of atoms so i have tried by
specifying A,B,C values both in [ atomtypes ] and [ pairtypes ] as
[ atomtypes ]
;name at.num mass charge ptype
A B C
CC32A 6 12.01100 0.1030 A 132277.5784
33.05785124 0.002710395
HCA2 1 1.00800 0.0355 A 29962.4608
41.58004158 0.000212547
OC30A 8 15.999400 -0.3480 A 243922.5976
40.2414486921 0.000803746
[ pairtypes ]
; i j func A
B C
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
Doing so , grompp is showing the following errors
ERROR 5 [file ffnonbondedpeo.itp, line 13]:
Too many parameters or not enough parameters for topology B
ERROR 6 [file ffnonbondedpeo.itp, line 14]:
Too many parameters or not enough parameters for topology B
Generated 6 of the 6 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'polymer'
ERROR 7 [file topol.top, line 1652]:
ERROR: The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist.
------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1372
Fatal error:
There were 7 errors in input file
-------------------------------------------------------
Any help will be highly appreciated.
Regards,
Ramesh Cheerla
--
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
