Dear Gromacs users,<br> <br> 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.<br>
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 <br><br>[ atomtypes ]<br>
;name at.num mass charge ptype A B C <br>CC32A 6 12.01100 0.1030 A 132277.5784 33.05785124 0.002710395<br>HCA2 1 1.00800 0.0355 A 29962.4608 41.58004158 0.000212547<br>
OC30A 8 15.999400 -0.3480 A 243922.5976 40.2414486921 0.000803746<br>[ pairtypes ]<br>; i j func A B C<br>OC30A OC30A 2 243922.5976 40.2414486921 0.000803746<br>
OC30A CC32A 2 179625.8144 36.297640653 0.001476115<br>OC30A HCA2 2 85489.9984 40.899795501 0.000413379<br>CC32A CC32A 2 132277.5784 33.05785124 0.002710395<br>CC32A HCA2 2 62955.3928 36.832412523 0.000759396<br>
HCA2 HCA2 2 29962.4608 41.58004158 0.000212547<br>;########### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6)<br>;D = A, B = 1/P, C = E<br><br> <br>Doing so , grompp is showing the following errors <br>
<br> ERROR 5 [file ffnonbondedpeo.itp, line 13]:<br> Too many parameters or not enough parameters for topology B<br><br><br>ERROR 6 [file ffnonbondedpeo.itp, line 14]:<br> Too many parameters or not enough parameters for topology B<br>
<br>Generated 6 of the 6 non-bonded parameter combinations<br>Excluding 3 bonded neighbours molecule type 'polymer'<br><br>ERROR 7 [file topol.top, line 1652]:<br> ERROR: The cut-off length is longer than half the shortest box vector or<br>
longer than the smallest box diagonal element. Increase the box size or<br> decrease rlist.<br>------------------------------------------------------<br>Program grompp, VERSION 4.5.5<br>Source code file: grompp.c, line: 1372<br>
<br>Fatal error:<br>There were 7 errors in input file<br>-------------------------------------------------------<br><br><br>Any help will be highly appreciated.<br><br><br>Regards,<br>Ramesh Cheerla<br>