VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 20 2009 - 10:38:17 CDT

On Tue, 2009-10-20 at 09:39 -0500, John Stone wrote:

hi,

one additional comment: while it is technically easy
to move the Mg _ion_(!) in VMD, it will most likely
result in clashes with the water positions, in case
you want to use the resulting configurations as starting
point for some sort of umbrella sampling or similar
calculation. if my guess is correct, than you would be
better off to use the steered MD module in NAMD to
generate a proper trajectory and have good starting
configurations at the spacing you desire. of course,
if you are after a free energy profile, you might just
do a number of steered MD runs right away, average
and inegrate over them and be done with it.

for whatever you want to do, just keep in mind, that
VMD only knows about geometries and nothing about modeling,
so it will just do what you ask it to do (which is a good
thing), but it may not be what you are looking for. software
does not have common sense. ;)

cheers,
   axel.

> Hi,
> Please have a look at the VMD tutorials, they describe how to use
> the atom selection commands to manipulate structures along the lines
> of what you want to do:
> http://www.ks.uiuc.edu/Training/Tutorials/
>
> The VMD User's Guide also contains many simple examples.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Oct 20, 2009 at 11:08:12AM +0200, priyodorshi satpati wrote:
> > Dear All,
> >
> > My system is phosphate and Mg into a water box. The phosphate is at
> > the center of the box. I want to fix the phosphate in place and move
> > the Mg atom away from the phosphate (along the vector joining
> > Phosphorous and Mg). Lets say i want to move Mg 0.15 Angstrom at each
> > step and save the corresponding pdb file. Eventually i will move the
> > Mg 1.5 angs and i will save 10 pdb files.
> >
> > Please let me know how can i do it.
> >
> > Thanks and regards
> >
> > Priyadarshi
> >
> > --
> > Dr. Priyadarshi Satpati
> > Biocomputing and Structure research Group,
> > Laboratoire de Biochimie,
> > Ecole Polytechnique,
> > 91128 Palaiseau, France
> >
> > Phone :
> > (Off) : +33/(0)1 69 33 48 94
> > (Mob) : +33/(0)6 27 75 56 49
> > (Res) : +33/(0)177069139
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.