Dear all, Regarding my question concerning the format of the [bonds] part of the topology file, I tried some new things: Changing the [bonds] part in the topology to: [ bonds ] ;ai aj func n 1 2 9 0
for n=0 (and therefore the file: table_b0.xvg) produces this error message:Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Bonds.But the other error message reported in the first post vanished.I would be really grateful if somebody could tell me how the line in the [bonds] part has to look like when using tabulated boned interactions.Do I for example have to specify the force constant reported in the 4.2.14 section of the manual (by simply writing it behind the n) ?Best,LizGesendet: Dienstag, 04. August 2015 um 14:41 Uhr
Von: "Liz Bell" <lizb...@gmx.at>
An: gromacs.org_gmx-users@maillist.sys.kth.se
Betreff: [gmx-users] tabulated bonded interaction functions-- 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.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 typesNo default Lin. Angle typesNo default Proper Dih. typesI 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
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