VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 07 2015 - 02:44:03 CST

On Jan 7, 2015 8:21 AM, "Dhritiman Talukdar" <dhritimant_at_gmail.com> wrote:
>
> I tried to save as mol2 file. but Avogadro was taking time.. I guess
there is no point in trying to convert the pdb to mol2 in OpenBable
although I tried it too..
> Please suggest any other file format I should try.

I gave a URL to the list of file formats supported by vmd in a previous
email.

>
> Now about the force fields... For the smaller systems I have been using
the parameters form the following paper:
> Interface of Grafted and Ungrafted Silica Nanoparticles with a
Polystyrene Matrix: Atomistic Molecular Dynamics Simulations
> Tinashe V. M. Ndoro, Evangelos Voyiatzis, Azadeh Ghanbari, Doros N.
Theodorou, Michael C. Böhm, and Florian Müller-Plathe
> Macromolecules 2011 44 (7), 2316-2327
> http://pubs.acs.org/doi/abs/10.1021/ma102833u
> pair_style lj/charmm/coul/charmm
> bond_style harmonic
> angle_style harmonic
> I have taken care of the units. I am using units style real
>
> On Wed, Jan 7, 2015 at 10:54 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
wrote:
>>
>>
>> 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--089e0122e70a017c05050c0bed5d--