From: Axel Kohlmeyer (
Date: Fri Jul 06 2012 - 23:05:45 CDT

On Sat, Jul 7, 2012 at 1:34 AM, satya kumar <> 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.


> Request you to guide me. Thanks for your time.
> With Regards,
> Satya.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.