VMD-L Mailing List

From: satya kumar (mail2mvskumar_at_gmail.com)
Date: Mon Jul 09 2012 - 08:15:51 CDT

Firstly thanks a lot for the help. The command "within 5 of nucleic" worked
and I need to save the coordinate file as a .gro file. Is there a way that
I can save this file from VMD?

With Regards,
Satya.

On Sat, Jul 7, 2012 at 12:05 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Jul 7, 2012 at 1:34 AM, satya kumar <mail2mvskumar_at_gmail.com>
> wrote:
> > Hello VMD users,
> >
> > I am working on Molecular Dynamics simulations. I have a file sample.gro
> > that has a box consisting of DNA molecule+water molecules in my system. I
> > have to choose all the water molecules that are close to the dna (with
> some
> > cut off distance). Is there a way that VMD selection can handle it?
>
> yes. the atom selection syntax has a "within <distance> of"
> as well as an "exwithin <distance> of" keyword and using
> the "same fragment as" expression selects entire molecules.
>
> all you have to do is to combine these with descriptions that
> match your water and DNA molecules and then you have
> your custom selections. for details, please have a close look
> at the examples and documentation of the atom selection
> syntax in the VMD user's guide.
>
> axel.
>
> >
> > Request you to guide me. Thanks for your time.
> >
> > With Regards,
> > Satya.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>