VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Oct 03 2014 - 14:32:48 CDT

On Fri, Oct 3, 2014 at 2:25 PM, Dave Schall <schalljd_at_gmail.com> wrote:
> Axel,
>
> How do you create the dummy atoms in topotools for output to lammps?
>
> Say I have a pdb file with molecule A having atom types A1 and A2 and
> molecule B having types B1 and B2.
>
> In a system with a mix of A and B my lammps coord file would have atoms
> tagged as A1=1, A2=2, B1=3, B2=4.
>
> If I have a system containing only B molecules, is there a way to make
> topotools dump the B atoms as lammps type 3 and 4 for lammps (instead of
> defaulting to 1 and 2) so I don't need to renumber everything in the lammps
> input script to match the coord file?

topotools was written under the assumption that this was not needed.
the interface to LAMMPS data files came later. i think at the moment
the best way is to postprocess the data file with an
awk/perl/python/tcl script and tell it to fix up what needs fixing up
based on parsing the comments for atom types.

i will have to think about what would be a good interface to tell
topotools to reserve space for certain atom/bond/etc. types.

>
> Dave
>
> On Fri, Oct 3, 2014 at 2:16 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Fri, Oct 3, 2014 at 1:21 PM, Josh Vermaas <vermaas2_at_illinois.edu>
>> wrote:
>> > Hi Dave,
>> >
>> > The issue here is actually something that is usually quite benign (I
>> > think).
>> > You say you are loading in pdbs, which normally don't have connectivity
>> > information (I dunno how packmol does it, but I don't see many with PDBs
>> > with conect records filled in). This means you are implicitly counting
>> > on
>> > VMD's bond-search algorithm to determine all of your connectivity. VMD's
>> > bond-search algorithm is efficient, which means it breaks down the N
>> > particles, and assigns them to grid patches based on their location in
>> > space
>> > (not the order they were loaded), searching for atoms that are close
>> > from a
>> > small subset of the system, vastly reducing the number of distance
>> > comparisons that need to be made. Now you said you let packmol make all
>> > of
>> > these systems independently, which means that by chance alone, some
>> > molecules are split across these patches differently in one structure
>> > relative to another. The order of the bonds stored internally will be
>> > different each time! You can test this by asking VMD to write out a psf
>> > after the bonds, angles and dihedrals have been guessed. I'm betting the
>> > order of the indices will not be sorted, and that the bondlists will be
>> > different for each system. Now topotools iterates linearly over this
>> > bondlist to build up angles and dihedrals, which I *think* is why it has
>> > this weird behavior. Why does the order of the angles and dihedrals
>> > matter
>> > though? Is this something LAMMPS specific? I'm also confused as to why
>> > the
>>
>> josh,
>>
>> this was not about the order of the angles and dihedrals, but the *types*.
>> a psf file doesn't even store that information, but it is crucial in
>> LAMMPS, because they are not referred to with a symbolic name but a
>> number. the symbolic names that were quoted are only comments. if you
>> want to use the same (bond/angle/dihedral) parameter definition for
>> multiple simulations of the same system, those names need to be
>> ordered, so the assigned numbers are the same.
>>
>> in fact, for systems with more variety, it may be needed to pad the
>> list for interaction types with dummies that are not present in a
>> specific topology to enforce the reuse of parameter files. with
>> CHARMM/NAMD this matching and assigning is all done at a later step
>> during the MD run. that has some advantages (it is simpler to create
>> the topology), but also some drawbacks (it requires that the bonded
>> interaction types are uniquely defined by the atom types comprising
>> that interaction).
>>
>> axel.
>>
>> > angles and dihedrals are specified based on what look like atomnames and
>> > not
>> > indices, but I'm sure its just a formatting thing.
>> >
>> > -Josh Vermaas
>> >
>> >
>> > On 10/03/2014 11:08 AM, Dave Schall wrote:
>> >
>> > Hi vmd-users,
>> >
>> > I am converting pdb files to a lammps coord files using vmd/topotools. I
>> > have a system with two types of molecules, say A and B. I am using
>> > packmol
>> > to generate pdb files for systems with different mole fractions of A and
>> > B.
>> > Packmol generates lists all the A molecules first then, all the B
>> > molecules
>> > after.
>> >
>> > I take this pdb file and read into vmd, do some atom selections to set
>> > charges/types/masses, etc. I have topotools guess the angles and
>> > dihedrals.
>> > Then I dump to a lammps coord file via topotools. I have a tcl script
>> > set up
>> > to do this the same way every time.
>> >
>> > Since I am running a fairly large set of simulations, I'd like this to
>> > be
>> > somewhat automated, but what I find when I inspect the lammps coord
>> > files is
>> > that the order of angles and dihedrals is not always the same. This
>> > means I
>> > have to check each coord file against my lammps input file to make sure
>> > the
>> > order of the parameters match.
>> >
>> > For example for some files I get:
>> >
>> > # 1 C3-C4-H1
>> > # 2 C-C1-H
>> > # 3 C1-C-H
>> > # 4 C2-C-H
>> > # 5 H1-C3-H1
>> > # 6 C-C2-H
>> >
>> > For some others:
>> >
>> > # 1 C3-C4-H1
>> > # 2 C-C1-H
>> > # 3 C1-C-H
>> > # 4 C2-C-H
>> > # 5 C-C2-H
>> > # 6 H1-C3-H1
>> >
>> > (5 and 6 as switched)
>> >
>> > Dihedrals are much more mixed up than angles.
>> >
>> > Am I wrong in assuming that if the order of molecules (and atoms
>> > therein)
>> > are the same in every pdb file they should be read in the same order by
>> > vmd/topotools? Is this some function of how "topo guessangles" and "topo
>> > guessdihedrals" works? If so I guess I better get busy building a a
>> > parameter database and script that can create input decks from lammps
>> > coord
>> > files.
>> >
>> > Thanks,
>> >
>> > Dave
>> >
>> >
>> >
>> >
>> > --
>> > J. David Schall, Assistant Professor
>> > Dept. of Mechanical Engineering, Oakland University
>> > 328 Engineering Center, Rochester, MI 48309
>> > 248-370-2870
>> >
>> >
>>
>>
>>
>> --
>> 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.
>
>
>
>
> --
> J. David Schall, Assistant Professor
> Dept. of Mechanical Engineering, Oakland University
> 328 Engineering Center, Rochester, MI 48309
> 248-370-2870 

-- 
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.