VMD-L Mailing List

From: Jim Parker (jimparker96313_at_gmail.com)
Date: Mon Mar 02 2015 - 21:20:19 CST

Hello Fred,
  Perhaps you have already resolved this, but here is a partial solution.
Typically, I select the atoms of interest

    set Sel1 [atomselect top "residue $myList"] ; # need only atoms of
interest
    set waterSel [atomselect top "water and element O"] ; # water
atoms at O posits only

where the keyword "water" will find all water molecules without specifying
a residue name.
there is a keyword "ion" for SOD (Na), and CLA (Cl) atoms, and probably
others but this was sufficient for my uses.
  set ionSel [atomselect top ion]

For the surfacant atoms, is there a common residue name for them in the
resulting .psf file?
Same question for the nanotube?

If not, you can make a list of residue numbers of interest
   set carbonList [ <tcl code to make an appropriate list of integers>] ;#
I'm used to python where the range() function is very handy
   set carbonSel [atomselect top "residue $carbonList"]

Additionally, I would recommend loading the .psf into VMD, and examining
the available selection names by Graphics->Representations. Then choosing
the "Selections" tab on the Graphical Representations dialog.

And then compute the RDF from
  set grAll [measure gofr $waterSel $Sel1 delta $dr rmax $maxR usepbc $pbc
selupdate 1 first $start last $end step $stride]

Cheers,
--Jim Parker

Department of Physics and Astronomy
The University of Texas at San Antonio

On Mon, Feb 23, 2015 at 3:31 PM, Phelan Jr., Frederick R. Dr. <
frederick.phelan_at_nist.gov> wrote:

> Hi,
>
>
>
> I have an atomistic system consisting of water, ions, surfactants, and a
> carbon nanotube. The surfactants assemble on the tube forming a complex. I
> would like to compute the RDF of the water wrt to the surfactants on the
> surface of the tube.
>
>
>
> The computation was done in LAMMPS. So, I created psf of the system using
> “topo readlammpsdata lammps.data full”; closed; read in the trajectory;
> read in the psf; and I am able to compute the rdf of just the hydrogen and
> oxygen in the water using “name 12” and “name 14” as the “selection 1” and
> “selection 2” entries, and it looks like what you would expect. So, I am
> confident I have that much correct.
>
>
>
> My question then is, how do I compute the rdf of the water molecules with
> respect to anything else? I am talking about VMD nomenclature here. I see
> that the individual molecules are showing up as residues. The water is
> essentially residue 101 thru 10,100. But, I think what I need something
> akin to the residuetype which in this case, unfortunately, has the value
> “nothing”.
>
>
>
> Many thanks,
>
> Fred
>
>
>
>
>
>
>
>
> ------------------------------
>
>
> *Frederick R. Phelan Jr., Ph.D. *Polymers & Complex Fluids Group
> Materials Science and Engineering Division
> National Institute of Standards and Technology
> ------------------------------
>
> NIST
> 100 Bureau Dr., STOP 8542
> Gaithersburg, MD 20899-8542
> 301.975.6761
> 301.975.4924 (FAX)
>
> frederick.phelan_at_nist.gov
>
> My Polymers & Complex Fluids Home Page
> <http://www.nist.gov/mml/msed/polymers/fred-phelan.cfm>
>
> WebFF Project Page <http://nist.gov/mml/msed/polymers/webff.cfm>
>
> [image: mml]
>
>
>
>
>


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