Re: How to confirm water box is big enough?

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Tue Mar 30 2010 - 17:36:12 CDT

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 - 05:22:51 CST