VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 06 2015 - 14:23:56 CST

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.
>>
>>
>