[gmx-users] tabulated bonded interaction functions

[Mark Abraham]

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 <LizBell at 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.abraham at gmail.com>
> *An:* gmx-users at 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 <LizBell at 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" <LizBell at gmx.at>
> > *An:* gromacs.org_gmx-users at 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
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