VMD-L Mailing List

From: nmichaud_at_jhu.edu
Date: Tue Aug 07 2007 - 11:54:20 CDT

As other people have mentioned, there is no way to use the standard
trajectory formats (dcd, xtc) for this purpose, since 1) they don't allow
for variable numbers of atoms per frame, and 2) the atom index is implicit
in the position of the coordinates in the overall array. Your only option
is to create your own binary data format where you can specify the number
of atoms at the start of each frame and store the atom index with each
atom. Of course then you have to write a reader for VMD, and possibly
modify other parts of VMD to let you specify/render only a subset of atoms
from the whole PSF for each frame.

Naveen

On Tue, 7 Aug 2007, Axel Kohlmeyer wrote:

> On Tue, 7 Aug 2007, [iso-8859-7] Θωμας [iso-8859-7] Ευαγγελιδης wrote:
>
> thomas,
>
> this does not work with .dcd at all, as john pointed out.
> you'd have to write a single frame .dcd _and_ .psf for each
> frame, since also VMD cannot handle that situation. see:
> http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/
> for a workaround.
>
> the only file format that would handle what you describe
> well is the LAMMPS atom style dump format, where each atom
> index is archived with the position (which makes it nasty
> to read in VMD, and requires the dumping of all atoms to
> be compatible with VMD to begin with). if the number of atoms
> per frame varies, you will for the time being have to find
> a different visualization package and/or help to make VMD
> handle this more gracefully (not easy, if you want to preserve
> the current efficiency in handling large numbers of atoms).
>
> the best way to reduce the size of a trajectory is to make
> this selection rather generous. i'm currently working on some
> script/plugin with GUI that will hook into the file loading
> process and allow you to read only a selection. however this,
> again, has the constraint that the number and index of the
> atom does not change and is pretty tricky to begin with
> (our group is working on huge coarse grained MD systems, where
> it can be difficult to load only a few frames into regular
> desktop). at the moment, you can do this pretty straight forward
> in batch mode on a file by file basis.
>
> if you want to visualize only the n-closest atoms out of that
> reduced selection, see the suggestion in my other mail.
>
> cheers,
> axel.
>
> TE> Dear John,
> TE> the concept was to write a plugin which creates smaller dcd files from bigger
> TE> ones by taking into account only the water molecules & ions which surround
> TE> the macromolecule. The user will give a cutoff distance, lets say 5 A, and the
> TE> program will find which atoms are within 5 A in the first frame, lets say N.
> TE> Then it will take frame No.2, find which N atoms are closer to the protein and
> TE> write them in the new dcd. Then frame No.3 , etc... Probably the most atoms out
> TE> of N will be the same in every frame, so those atomIDs writen in the dcd will be
> TE> the same too, but there will be also some others which will be raplaced. Thus
> TE> the program will have to write these new atomIDs in place of the others.
> TE> Could it be possible for that new dcd file to hold a time-varying set of atoms
> TE> if we would create in some way a new psf file - or even by keeping the initial-
> TE> that will contain information about all the atoms seen in all the frames of the
> TE> new dcd? Do you have anything else to propose?
> TE> thanks,
> TE> Tom
> TE>
> TE>
> TE> Αρχικό μήνυμα από John Stone <johns_at_ks.uiuc.edu>:
> TE>
> TE> > Hi,
> TE> > Is there some specific reason you need to create a DCD file?
> TE> > One of the problems you're going to have with attempting to write
> TE> > out a time-varying set of atoms to a DCD is that you'll lose track
> TE> > of which atom indices are which. Why not just emit your own file format
> TE> > and use just the atoms you care about? The DCD format really isn't
> TE> > suited to holding a time-varying set of atoms, even with a big hammer ;-)
> TE> >
> TE> > The internal code in VMD does not calculate minimums nor maximums,
> TE> > but merely tests candidate atoms to see if they meet the distance
> TE> > selection criteria or not, for the currently active timestep.
> TE> > Calculating min, max, quantiles, or the histogram of distance for
> TE> > each atom over all timesteps would have to be done with your
> TE> > own script presently. If there is sufficient interest in adding
> TE> > a new "measure" subcommand for computing distances we could add one,
> TE> > but I haven't had any requests for such a feature thus far.
> TE> >
> TE> > Cheers,
> TE> > John Stone
> TE> > vmd_at_ks.uiuc.edu
> TE> >
> TE> > On Tue, Aug 07, 2007 at 12:52:34AM +0300, wrote:
> TE> > >
> TE> > > Hi,
> TE> > > I am writing a plugin for VMD and I need some help. What I am trying to do
> TE> > is to
> TE> > > create dcd files which contain only the atoms that are within a given
> TE> > cutoff
> TE> > > distance from the protein. The problem is that each frame of a dcd must
> TE> > contain
> TE> > > the same number of atoms, so if frame No.1 contains N atoms then I have to
> TE> > find
> TE> > > which N atoms of frame No.2 are closer to the protein and write only them
> TE> > in
> TE> > > the new dcd file. My question is if the "atomselect top "exwithin $cutoff
> TE> > of
> TE> > > protein"" command calculates by default the minimum distance of each atom
> TE> > it
> TE> > > selects from the protein and if there is a way to retrieve it from the
> TE> > source
> TE> > > code. I tried to read the source code but I am not sure if it does what I
> TE> > need.
> TE> > > I just figured out that the "within" macro functions by creating grid cells
> TE> > > enclosing the protein atoms (others) as well as the atoms which souround
> TE> > them
> TE> > > (flgs). I have also some other ideas but that would be the faster way to
> TE> > find
> TE> > > the atoms I need.
> TE> > > I would appreciate any help,
> TE> > > Thomas Evangelidis
> TE> >
> TE> > --
> TE> > NIH Resource for Macromolecular Modeling and Bioinformatics
> TE> > Beckman Institute for Advanced Science and Technology
> TE> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> TE> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> TE> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> TE> >
> TE>
> TE>
> TE>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>