Dear all,
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:
No default Tab. Bonds NC types
No default Lin. Angle typesNo default Proper Dih. types
I think Gromacs can not find the values that I defined in the table_b*.xvg, table_a*.xvg and table_d*.xvg.
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?
Does anybody know how to adapt the topology file, or whether some additional lines are needed in the mdp files?
Thank you very much in advance,
Liz
-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
