VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 06 2015 - 23:24:11 CST

On Jan 7, 2015 5:41 AM, "Dhritiman Talukdar" <dhritimant_at_gmail.com> wrote:
>
> 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

No, it isn't.

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 repeat, it is a _very_ bad idea to use the pdb file format for such a
large structure.

>
> I will try with the Tersoff force field.

I don't understand this statement. You will have to know which force field
you want to use _before_ you start building a topology and not the other
way around.

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

Nonsense. It works fine.

>
> 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.
>> >>
>> >>
>> >
>
>