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On 15/02/2012 5:42 PM, ramesh cheerla wrote:
<blockquote
cite="mid:CAPNFZqdeLP=D58cS5cCaZE2heK9=g05e_7MO5M-YLcjiqQN4dg@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
With [ nonbond_params], not [atomtypes] or [pairtypes]. See table
5.4 of section 5.7.1 of manual.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPNFZqdeLP=D58cS5cCaZE2heK9=g05e_7MO5M-YLcjiqQN4dg@mail.gmail.com"
type="cite">
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>
<br>
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<br>
</blockquote>
<br>
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