VMD-L Mailing List

From: Dhritiman Talukdar (dhritimant_at_gmail.com)
Date: Tue Jan 06 2015 - 22:41:41 CST

I realize that none of the atoms should have more than 4 bonds in the
structure and it doesn't.. But the total number of bonds is large so maybe
that is the problem. Also, I am having no problems with 32*32*32 file or
lower. After using "topo retypebonds" and "topo bondtypenames", VMD shows
only Si-O bond.

The pdb file was made in Avogadro by adding a unit cell and then using
Supercell Builder. Before saving the unit cell was removed.

I will try with the Tersoff force field.

Also automatic bond suppression by autobonds off filebonds off is not
working in VMD text mode in a linux intel HPC.

On Wed, Jan 7, 2015 at 1:53 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
> On Jan 6, 2015 9:03 PM, "Josh Vermaas" <vermaas2_at_illinois.edu> wrote:
> >
> > Hi Dhritiman,
> > How was your pdb constructed? This system really shouldn't have all that
> many bonds (think about it, the lattice shouldn't have more than 4 bonds
> per atom...), so I'd look more closely at how the system was constructed
> rather than spend your time recompiling VMD.
>
> More importantly, if this is a malformatted pdb file, recompiling vmd will
> not solve anything. Vmd won't complain, but the structure will be garbage.
>
> Also, for some SiO2 force fields that lammps supports (e.g. Tersoff),
> there must not be bonds in the.topology and thus automatic bond generation
> must be suppressed.
>
> > -Josh Vermaas
> >
> >
> > On 01/06/2015 12:15 PM, Dhritiman Talukdar wrote:
> >>
> >> The system I am referring to is a 37*37*37 Silica Cube. (37 being the
> number of SiO2 i.e. 37 Si and 74 O).
> >> I need it for finally making a spherical silica nanoparticle. The
> sphere will be sculpted out using LAMMPS.
> >> I will compile VMD in Linux. May be it will be easier there.
> >>
> >> On Tue, Jan 6, 2015 at 9:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>>
> >>> On Tue, Jan 6, 2015 at 10:36 AM, Dhritiman Talukdar
> >>> <dhritimant_at_gmail.com> wrote:
> >>> > Hi,
> >>> > I need to load a large pdb file in VMD. when I try it VMD gives the
> >>> > following error:
> >>> >
> >>> > MolAtom xxxx: Exceeded maximum number of bonds
> >>> >
> >>> > I have learned that the VMD provides space for 8 bonds per atom.
> This limit
> >>> > is coded into the program as a constant, but by a simple recompile,
> it can
> >>> > be increased to an arbitrary number.
> >>>
> >>> what kind of a system do you have that requires more than 8 bonds *per
> >>> atom*??? that is *very* unusual.
> >>>
> >>> since you have a "large system", it is more likely that your PDB file
> >>> is actually not standard conforming and thus not readable except for a
> >>> correct PDB reader
> >>> PDB is not really a file format meant to be used for large system.
> >>> better to use a more flexible file format.
> >>>
> >>> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
> >>>
> >>> > Can somebody please recompile VMD with a higher limit say 50 or so..
> >>> > I am using windows 7 32 bit OS.
> >>>
> >>> not likely going to happen unless you do it yourself.
> >>>
> >>> axel.
> >>>
> >>> > Thanking you in advance..
> >>> > Dhritiman Talukdar
> >>> > dhritimant_at_gmail.com
> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >>> College of Science & Technology, Temple University, Philadelphia PA,
> USA
> >>> International Centre for Theoretical Physics, Trieste. Italy.
> >>
> >>
> >
>