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. 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
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