"mdrun -table table" means the prefix for tables is table, so it will look for tables like 'table_b0.xvg', etc.
Peter On 06/08/15 08:56, Liz Bell wrote: > Hello, > there was indeed a mistake in my [angles] entry but the basic > implementation works like described below. > Grompp now works perfectly. Thank you very much for confirming me that > the basic implementation was correct. > > But now I have another question: How do I include the tables of the > bonded interaction functions in mdrun? > Simply > "mdrun" > does not work. Using the command "-table" like > "mdrun -table table_b0.xvg table_b1.xvg table_b2.xvg table_a0.xvg > table_a1.xvg table_a2.xvg table_a3.xvg table_d0.xvg table_d1.xvg > table_d2.xvg table_d3.xvg" > or > "mdrun -table table*.xvg" > does not work neither. > Anybody an idea? > > Thanks, > Liz > *Gesendet:* Dienstag, 04. August 2015 um 16:07 Uhr > *Von:* "Mark Abraham" <mark.j.abra...@gmail.com> > *An:* gmx-us...@gromacs.org > *Betreff:* Re: [gmx-users] tabulated bonded interaction functions > Hi, > > I believe your [angles] entries should work, but I've never tried it, > and I > could easily believe that a bug exists. This is code that the developers > rarely use. > > If you're confident you got that output from a correctly-formed [angles] > section, then please open a report at http://redmine.gromacs.org, attach > the necessary files in a tarball and we can get to the bottom of it. > > Thanks, > > Mark > > On Tue, Aug 4, 2015 at 3:55 PM Liz Bell <lizb...@gmx.at> wrote: > > > Thank you for your response. > > > > The column "Order of parameters and their units" of table 5.5 states > that > > I have to include a value for n and the force constant k. > > I tried it by simply setting k to 1: > > [ bonds ] > > ;ai aj func n k > > 1 2 9 0 1 > > > > it produces a similar error message (now for the angles instead of the > > bonds): > > Fatal error: > > Incorrect number of parameters - found 1, expected 2 or 4 for Tab. > Angles. > > > > (I also added the n and k in the [angles] part like: > > [ angles ] > > ; ai aj ak angleTyp n k > > 1 2 3 8 1 1 > > because of the fact that table 5.5 also states that I have to include a > > value for n and the force constant k for the angles. > > ) > > Any idea if I have to secify further values? (Some which are not in > table > > 5.5) > > Or does anybody know the activator for such an error message? > > > > Thank you in advance! > > Best, > > Liz > > *Gesendet:* Dienstag, 04. August 2015 um 15:33 Uhr > > *Von:* "Mark Abraham" <mark.j.abra...@gmail.com> > > *An:* gmx-us...@gromacs.org > > *Betreff:* Re: [gmx-users] tabulated bonded interaction functions > > Hi, > > > > Yes you have to specify k. That detail is in table 5.5, to which that > > section refers you. > > > > Mark > > > > On Tue, Aug 4, 2015 at 3:26 PM Liz Bell <lizb...@gmx.at> wrote: > > > > > 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, > > > Liz > > > > > > > > > *Gesendet:* 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 > > > > > > > > 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 types > > > No 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. > > > -- > > > 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. > > -- > > 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. > > -- > > 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. > -- > 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. > >
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