From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 06 2010 - 19:55:33 CDT

On Thu, 2010-05-06 at 12:21 -0400, Fatemesadat Emami wrote:
> Dear Axel,
> Thanks for your reply,

please always reply to the list so that everybody can see
how the problem was resolved. otherwise i usually don't reply
unless it is the first time or it is of personal concern.

> I looked at volmap tool. It is very useful if I can get the average
> density map out of my 2000 pdb file.
> Here is my problem excatly:
>
> I have simulated some systems including "peptide on a surface" by
> LAMMPS. After that I realized I can produce some nice representations
> with vmd. However, since my systems include surface, I could not
> produce an atribued .psf file to be able to load my trajectories

to get a simple psf from your lammps topology:

topo readlammpsdata data.mydata full (or whatever atom style you use)
animate write psf mydata.psf

but you don't really need a .psf file to use VMD.
it is only that most examples in the VMD manual show
psf files. that is just because those were generated
with NAMD and NAMD produces .psf and .dcd.

> into the vmd (I know I can build my systems in vmd but I do not want
> to repeat the lengthy simulations and just want to use what I have).
> What I did was to write a code to produce single .pdb files (including
> just the peptide) from each snapshots.

what a waste of time and diskspace. as an alternative to the
scheme from above, you could have taken just one .pdb file
and then written out the .psf file.

> Then I all of loaded them into vmd to superimpose them (trying to see
> the average conformation). Finally I need to render some

have a closer look at RMSD trajectory tool. it might be
very helpful in this context.

> representetive pictures.
>
> knowing that, can I still use volmap to get the density map of 2000
> molecules (load from 2000 pdb files).

i am not sure what you are saying here, but if it satisfies
your needs that it is good.

cheers,
    axel.

> I thank you for your helps,
> Fatima
>
>
> On Wed, May 5, 2010 at 10:39 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> On Wed, May 5, 2010 at 7:35 PM, Fatemesadat Emami
> <fe2_at_zips.uakron.edu> wrote:
> > Dear vmd users,
> > I have several pdb files pertaining to different snapshots
> of one MD run
> > (structures are exactly the same). Their names are in the
> format of
> > SNAP1.pdb, SNAP2.pdb , ...
> > I want to select first residue (e.g. LYS) of all them in one
> selection
> > altogether; Is that possible.
>
>
> no.
>
> > In fact, I want to add surf just around the first residue (I
> can do that
> > with tcl one by one but take a bit of time for vmd to load
> 2000 files along
> > with the surfaces).
> > What I am using now is:
> >
> > for {set i 30} {$i < 2006} {incr i} {
> > set filename [concat SNAP$i.pdb]
> > mol new $filename waitfor all
> > mol representation surf 1
> > mol Material Glass1
> > mol selection {resname LYS}
> > mol addrep top
> > }
>
>
> i don't think this would make much sense.
>
> if you are looking for some kind of density distiribution
> over the trajectory - and your script looks like a *very*
> crude version of that - you should have a look at the
> volmap tool and then use an isosurface for the resulting
> grid file. that is usually giving a much better representation
> of what is happening then stacking 2000 transparent objects
> on top of each other...
>
> cheers,
> axel.
>
>
> >
> > I was wondering if I can improve doing that!
> >
> > Many thanks
> > Fatima
> >
> > Yours Sincerely,
> > Fateme Sadat Emami
> > Nano Scale Laboratory
> > Polymer Engineering Department
> > The University of Akron
> >
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
>
> --
> Yours Sincerely,
> Fateme Sadat Emami
> Nano Scale Laboratory
> Polymer Engineering Department
> The University of Akron

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.