VMD-L Mailing List

From: p.w.fowler_at_qmul.ac.uk
Date: Fri Feb 13 2004 - 17:04:08 CST

Bamidele,

There are a couple of ways to do this - it depends upon what you mean by
_remove_ the water molecules.

(i) In the Selected Atoms box in the Graphics | Representations box, put 'not
water'; this will only visualise the oligomer
(ii) Alternatively, via the Tcl interface you may permanently delete the water
molecules using delatom.

I reckon you want the first option. Check out the VMD manual

http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html

and the SummerSchool tutorials.

http://www.ks.uiuc.edu/Research/vmd/current/tutorial/html/

--Phil

> hi,
> i want to view the trajectory of a phenylacetylene oligomer solvated in a
> box of water.
> but because there are so many water molecules surrounding the oligomer,
> it's almost impossible to see what's
> going on to the oligomer, which is located at the center of the box of
> water.
> is possible to remove the surrounding water molecules in vmd so i can view
> the oligomer clearly?
> thanks in advance,
> dele
>
> ______________________
> Dept of Chemical Engineering
> Clemson University
> Clemson, SC 29634-0909
> ______________________
>
>