VMD-L Mailing List

From: Dhritiman Talukdar (dhritimant_at_gmail.com)
Date: Wed Jan 07 2015 - 01:21:31 CST

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.

Now about the force fields... For the smaller systems I have been using the
parameters form the following paper:

   1. 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.
> >> >>> 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.
> >> >>
> >> >>
> >> >
> >
> >
>