----------------------------------------
> Date: Thu, 29 Nov 2012 08:58:50 -0500
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Electrostatic field in atoms - GROMACS is not
> reading table interaction functions for bonded interactions
>
>
>
> On 11/29/12 8:18 AM, Ariana Torres Knoop wrote:
> > Dear GROMACS users,
> >
> > We are trying to determine the electric fields at the C and N atoms in a
> > protein. To do so, we thought of performing a one step energy minimization
> > with the Lennard-Jones as well as the bonded interactions turned off, in
> > order to get only the coulomb forces.
> > For that, according to
> > www.gromacs.org/Documentation/How-tos/Tabulated_Potentials , we made a
> > table (table.xvg) in which the Lennard-Jones potential was set to zero and
> > we also made three tables (table_b1.xvg, table_a5.xvg and table_d5.xvg)
> > according to section 4.2.13 of the Manual (Tabulated interaction
> > functions), in which the f(x)=0 for the whole range of distances, angles,
> > dihedrals present in the simulation box. The numbers 1, 5, 2 correspond to
> > the function number referred to in the topology file. For example for the
> > bonds interaction, in the topology file we have:
> > [ bonds ]
> > ; ai aj funct c0 c1 c2 c3
> > 1 2 1
> > 1 3 1
> > 1 4 1
> > 1 5 1
> > 5 6 1
> > .
> > .
> > .
> > so we named the table "table_b1.xvg".
> >
> > We changed the run.mdp file as follows:
> > vdw-type = User
> > coulombtype = PME-User
> >
> > And then we try to run it using:
> > mdrun -v -deffnm run.tpr
> >
> > When checking the energy contribution using g_energy, Lennard-Jones
> > contribution was indeed zero, but
> > for the bonded interactions this is not the case:
> >
> > Energy Average Err.Est. RMSD Tot-Drift
> > -------------------------------------------------------------------------------
> > U-B 18180.1 -- 276.416 -540.638 (kJ/mol)
> > Proper Dih. 11732.3 -- 27.6829 -54.0396 (kJ/mol)
> > Improper Dih. 1027.26 -- 47.1598 -91.7097 (kJ/mol)
> > LJ-14 0 -- 0 0 (kJ/mol)
> > LJ (SR) 0 -- 0 0 (kJ/mol)
> >
> > We though that maybe the tables for the bonded interactions were not taken,
> > so we tried:
> > mdrun -v -tableb table_b1.xvg table_a5.xvg table_d2.xvg -deffnm run.tpr
> >
> > But it also did not work.
> >
> > We are not sure whether the problem is in the table definition, the way of
> > running the program, the run type, the name of the tables, or if there
> > should be some other modifications in the *mdp file.
> >
> > We would be very grateful if anyone could help us out here.
> >
>
> I think the problem comes from the fact that the function types you are
> specifying in the topology correspond to actual potentials and thus the tables
> are being ignored. Per Table 5.5, it seems that any value for the table is
> acceptable (n >= 0) but using numbers corresponding to actual function types
> may
> not work. The specified format also requires that both the table number and
> force constant (k) be specified in the topology, but the [bonds] section you
> show above has no value of k and the function type corresponds to a simple
> harmonic bond. There is no "bond" energy in the output, which suggests you are
> using constraints - is that the case?
No, the issue is that you are using function type 1. Tabulated bonds are
function type 8 or 9,
that is what should be in the 3rd column.
The actual number for the table file should appear after that in the 4th column.
Cheers,
Berk
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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