Re: Water molecules inside protein?

From: Stephen Hicks (
Date: Wed Jun 06 2007 - 11:04:28 CDT


Indeed, that sounds a bit more complicated, but it still seems
tractable. At worst, you will have waters interacting with a
different image of the protein than the one NAMD is tracking. If you
didn't unwrap the boundaries, then (as far as I understand - please
correct me if I'm wrong!) you face the problem that the protein could
appear to be chopped in two if it's halfway across the boundary, so
you definitely want to keep the protein unwrapped. Perhaps you could
manually translate the waters into the unit cell *closest* to the
protein center? I'm not entirely sure how to access it, but if there
were a way to find the unit cell dimensions at any given frame (as
long as useFlexibleCell is off, this is trivial I suppose) then it's
as simple as *not* unwrapping the waters, and then finding the image
of the protein center in the primary unit cell. Anything more than
halfway across the cell from that center should be translated to an
adjacent cell.

For example, suppose your cell has dimension 2 on each side and is
centered at the origin. So it is a cube with opposite corners at
(-1,-1,-1) and (1,1,1). If your protein has diffused to, say
(1.5,0,0), then this has an image at (-0.5,0,0) in the primary cell.
So any waters with x<-0.5 should be translated by (2,0,0) to be closer
to the primary image of the protein. You can deal with the y and z
directions separately. In any case, whether or not you unwrap the
boundaries will not change any of the dynamics: only the way in which
coordinates are reported.


On 6/6/07, <> wrote:
> Hi Steve,
> Thanks for your reply but I am interested in new waters coming in and going out from center of my protein. Unwrapping the all things is not going to help because water will diffuse away due to unwrapping thing. I am not interested in seeing my protein stationary, i know it can be done by fit. I dont think so doing fitting the way you told is going to show me real waters interacting with protein all the time? CORRECT ME in case i misunderstood.
> Thanks again
> Harish
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
> ----- Original Message -----
> From: Stephen Hicks <>
> Date: Tuesday, June 5, 2007 10:07 pm
> Subject: Re: namd-l: Water molecules inside protein?
> > Harish,
> >
> > I'm not entirely sure I understand what you're asking, but if you're
> > just looking to track the water molecules, then unwrapping boundaries
> > for the entire system should be sufficient. You can use your initial
> > frame as a reference, and then for each successive frame measure the
> > fit back to the reference frame for just the protein and apply that
> > transformation to all molecules, including all the waters. This will
> > make things look like your protein is more or less stationary.
> >
> > -steve
> >
> > On 6/5/07, <> wrote:
> > > Hi All,
> > > I have been doing an NVE run of my protein with periodic
> > boundary conditions and my protein slowly moves during run, goes
> > out and wrapped to another side of box. ALl that is fine. I want to
> > track the water molecules in the center of protein during all
> > frames. I dont know how to tack them when protein itself is moving
> > and wrapped too. I am not sure doing unwrapping only protein or all
> > system can help anyhow? ANy help from experienced users will do great.
> > > HARISH
> > >
> > > -------------------------------------------------
> > > Harish Vashisth (Ph.D Candidate)
> > > CAT-361,Chemical & Biological Engg.
> > > Drexel University, Philadelphia, PA
> > > office: 215-895-5823
> > >
> > >
> >

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