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<pre>Dear all,</pre>
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<pre>I am perfoming MD simulations of P3Ht chains and I would like to define the bonded as well as the nonbonded parameters using tables.
Regarding the bonded parameters, there are no problems until now, as I simply wrote some additional lines in the mdp file (similar to this explanation: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials).
But how do I tell gromacs to use the information for [bonds], [angles]... (all the bonded potentials)... from table_b0.xvg for example.
The first line of the [bonds] section in my topology file looks like:
[ bonds ]
;ai aj func
1 2 9
Where 1 and 2 are the atoms and 9 is the function type.
Running grompp produces various of those mistakes:
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<div>No default Tab. Bonds NC types</div>
No default Lin. Angle types</div>
<div>No default Proper Dih. types</div>
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<div>I think Gromacs can not find the values that I defined in the table_b*.xvg, table_a*.xvg and table_d*.xvg.</div>
<pre>The section 4.2.12 in the gromacs manual tells "...for a bond with n=0 [...] the table is read from the file table_b0.xvg.
But where do I have to specify that the atoms 1 2 have the bonds with n=0, with the information provided in the table_b0.xvg?</pre>
<div>Does anybody know how to adapt the topology file, or whether some additional lines are needed in the mdp files?<br/>
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<div>Thank you very much in advance,</div>
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<div>Liz</div>
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