From: hl332_at_drexel.edu
Date: Wed Jun 06 2007 - 10:25:16 CDT
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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