From: wayj86 wayj86 (wayj86_at_gmail.com)
Date: Tue Jun 30 2009 - 03:36:49 CDT
Thank you very much for your answer. By doing what you introduced I
understand that even moved out, the protein was still in the water. However,
when protein moved out of its original water box and entering next cell, it
might interact with its image ("Ideally, one should work with a box which is
large enough that the protein does not interact with its image in the next
cell if periodic boundary conditions are used." --from NAMD tutorial). So I
measure the size of my protein and water box in one frame:
>Main< (smd) 54 % set p [atomselect top protein]
atomselect0
>Main< (smd) 55 % set w [atomselect top water]
atomselect1
>Main< (smd) 56 % measure minmax $p
{-5.25099992752 -21.2350006104 -42.3390007019} {100.650001526 43.7840003967
7.90799999237}
>Main< (smd) 57 % measure minmax $w
{-21.0270004272 -51.1430015564 -27.1930007935} {141.848007202 41.1160011292
43.9269981384}
I guess the distance on Z direction between the protein and its next image
was [43.93-7.90-(42.34-27.19)]=20.88A. I don't know how close the protein
and its image would cause the unwanted interactions. Do you have any advice
for that? Thank you in advance.
2009/6/30 Roman Petrenko <rpetrenko_at_gmail.com>
> Please, keep in mind that if you are using periodical boundary
> conditions (PBC), the protein is _always_ submerged in water due to
> periodicity of the system. Load your trajectory in VMD, and then you
> can see other images of your system by
> Graphics->Representations->Periodic and then check +Z and -Z.
>
>
>
> On Fri, Jun 26, 2009 at 4:02 AM, wayj86 wayj86<wayj86_at_gmail.com> wrote:
> > Dear all,
> >
> > I found it is difficult to make sure the protein keep in the water box
> > during the whole SMD process unless with a very big box. Now my protein
> went
> > out of the box with more than 10 residues and 14 angstrom off the water
> > boundary in the -Z direction. The distance between the "went-out" part
> and
> > the protein in the next cell was 13 angstrom. I have red the NAMD
> tutorial
> > but still want to ask you some questions:
> >
> > (1) Althought the protein should be merged in the water box when imposing
> > periodic boundary conditions, was the "went_out" phenomenon completely
> > unacceptable?
> >
> > (2) In my situation, would it have a bad effect on my result? Do I have
> to
> > redo the SMD again?
> >
> > (3) Is there any literature about this phenomenon which explain it in
> > detailed?
> >
> > Thank you in advance.
> >
> > --
> > The future is now!
> >
>
>
>
> --
> Roman Petrenko
> Physics Department
> University of Cincinnati
>
-- The future is now!
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