Re: Water molecules inside protein?

From: hl332_at_drexel.edu
Date: Wed Jun 06 2007 - 11:25:40 CDT

HI Steve,
 Yes, i want to do soemthing like you suggested. Thanks for this detailed mail, i understood what you want to communicate. I was thinking something on similar lines but was not sure how correct even that thing would be. Now, two people thinking the same way, things should be right. I will give it a try but I need to see how to unwrap individual waters.
Regards
Harish
-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: Stephen Hicks <shicks_at_ccmr.cornell.edu>
Date: Wednesday, June 6, 2007 12:04 pm
Subject: Re: namd-l: Water molecules inside protein?

> Harish,
>
> 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.
>
> -steve
>
> On 6/6/07, hl332_at_drexel.edu <hl332_at_drexel.edu> 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 <shicks_at_ccmr.cornell.edu>
> > 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, hl332_at_drexel.edu <hl332_at_drexel.edu> 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.
> > > > THANKS AND REGARDS
> > > > HARISH
> > > >
> > > > -------------------------------------------------
> > > > Harish Vashisth (Ph.D Candidate)
> > > > CAT-361,Chemical & Biological Engg.
> > > > Drexel University, Philadelphia, PA
> > > > office: 215-895-5823
> > > >
> > > >
> > >
> >
> >
>

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