[gmx-users] tabulated bonded interaction functions

[Mark Abraham]

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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