---- Original Message ----
From: Mohamed Osman <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Thursday, January 11, 2007 10:49:29 PM
Subject: [gmx-users] box size for simulation of membrane protein
My questions:
1. Protein is closer to one edge than the other. Does this make any
difference?
The solvants are part of equilibritaed lipid.
-Shouldn't do. It's still the same distance from its periodic image on each
side, which is what matters. As long as it's in the correct place in the
bilayer, I don't believe there are any 'edge effects' in the implementation of
PBC in gromacs you need to worry about.
Along protein axis:
a. The periodic image is 1.43 nm away. (along protein axis)
b. The distance between the protein and its mirror image is: 0.8 nm on
one side and 2.0 nm on the other side? (These affect PME - coulmb
interactions). Will these cause trouble?
-The minimum protein-image distance is all that matters. It doesn't matter how
close the protein is to one side of the box - if it's closer on one side, it's
further on the other. Unless you mean different distances on the x and y axis?
-As far as I know, PME sums out to infinity, so you can't really change that.
BUT:
2. Is it necessary to keep the protein at least 1.5 nm away from the edges
normal to z-axis? This more than doubles the number of solvant molecules.
----
I have simulations with less than 50,000 atoms (protein, solvants, and KcsA).
But no one realy says much about the box sizes.
What is the common practice? Please give examples?
and
How much compromise is acceptable ?
-The official requirement is for the minimim distance from protein to its
periodic image to be double the cutoff, so that no atom feels forces from more
than one image of the protein. However, you can probably get away with
reducing that minimum distance to slightly more than the cutoff (1.5nm in your
case) which just stops the protein from interacting with its own periodic
images. Most people work on this basis, on the grounds it probably doesn't
matter if the water molecules are 'feeling' more than one protein. It's a
judgement call really, depending on how badly you want it to run faster vs how
much you lose by making it do that.
"It is common to compormize in this respect !!!"
Thanks
Mohamed Osman
=======================
Professor of Electrical Engineering
Washington State University
Pullman, WA 99164-2752
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
____________________________________________________________________________________
Do you Yahoo!?
Everyone is raving about the all-new Yahoo! Mail beta.
http://new.mail.yahoo.com
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
