From: Jin Liu (jliunih_at_gmail.com)
Date: Tue Mar 30 2010 - 17:48:37 CDT
Hi Giacomo,
Thank you very much for the explanation. Now I understand it. Thanks.
Jin
On Tue, Mar 30, 2010 at 6:36 PM, Giacomo Fiorin
<giacomo.fiorin_at_temple.edu>wrote:
> Hi Jin, basically, when there is a residual electrostatic field from
> the protein, you will have that each water molecule will orient itself
> according to this field. When the number goes to zero, it means that
> the field is too small, or absent at all, and water molecules are
> disordered as they should be in a bulk environment.
>
> When I wrote that it's one of the best checks (not the only one), I
> meant that it's an analysis that you perform on your actual
> trajectory, rather than on a priori considerations.
>
> Concerning the conservation of the minimum distance between periodic
> images of the proteins, you can use VMD, with, for example, "measure
> contacts" and a little bit of scripting. I'm not aware if there is
> already a script available for this. You can also check the g_mindist
> tool in Gromacs, with the option "-pi" does exactly what you're
> looking for.
>
> Giacomo
>
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> mail: giacomo.fiorin_at_gmail.com
> ---- ----
>
>
>
> On Tue, Mar 30, 2010 at 6:09 PM, Jin Liu <jliunih_at_gmail.com> wrote:
> > Hi Giacomo,
> > Many thanks for the help. Is it possible that you could explain a little
> > more about "the average
> > projection of the water molecules' dipole moments on the distance vector
> > from the protein"? Why is this the best checks? When this number goes to
> > zero, it means no electrostatics interaction between images? And how to
> > check this number? Thanks.
> > Jin
> >
> >
> > On Tue, Mar 30, 2010 at 5:38 PM, Giacomo Fiorin <
> giacomo.fiorin_at_temple.edu>
> > wrote:
> >>
> >> Hi Jin, ideally, you'll want that two periodic images of the protein
> >> are always farther than twice the van der Waals cutoff: this way they
> >> would not only be out of range for their mutual interaction, but also
> >> that they don't interact with the same water molecules.
> >>
> >> If you used 10 Å as cutoff, you should be almost fine (give or take 1
> >> water molecule). FYI, it is becoming much more commonplace to use a
> >> larger cutoff (e.g. 12 Å).
> >>
> >> One thing you can do to make sure, is to compute the average
> >> projection of the water molecules' dipole moments on the distance
> >> vector from the protein. If the number goes to zero before the 10 Å
> >> maximum distance, in my opinion it's one of the best checks that you
> >> can provide.
> >>
> >> Giacomo
> >>
> >> ---- ----
> >> Giacomo Fiorin
> >> ICMS - Institute for Computational Molecular Science
> >> Temple University
> >> 1900 N 12 th Street, Philadelphia, PA 19122
> >> work phone: (+1)-215-204-4216
> >> mobile: (+1)-267-324-7676
> >> mail: giacomo.fiorin_at_gmail.com
> >> ---- ----
> >>
> >>
> >>
> >> On Tue, Mar 30, 2010 at 3:29 PM, Jin Liu <jliunih_at_gmail.com> wrote:
> >> > Hi,
> >> >
> >> > I did a few MD simulations with the the minimum distance from the
> >> > protein to
> >> > the edge of the water box as 10 angstrom. The simulations ran smoothly
> >> > without any problem. I am wondering what I could do to confirm the
> water
> >> > box
> >> > is big enough? Should I measure the distance between the protein and
> its
> >> > image in the other boxes during the simulation? Or what else can I do
> to
> >> > convince people that the water box is not too small?
> >> > Thank you very much.
> >> > Best regards,
> >> > Jin
> >> >
> >> >
> >
> >
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:58 CST