[gmx-users] tabulated bonded interaction functions

[Peter Kroon]

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