Subject: Summary: Water Box (MD)

From: Fdo Danilo Gonzalez Nilo <[email-masked]>
Date: Thu, 20 Mar 1997 08:33:22 -0400 (CST)

Hi!
	It's the summary of the answers, about the following question:

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	We are runnig a dynamic Calculation of a macroion with 8 positive 
charges in a water box, using PBC and a 30x30x30 cell, T=300 K, 50ps.
	We observe many water molecules going out from the box, during 
the process. We don't use any counterion.

Is it normal that in the PBC condition, water molecules go out the cell?
if not.... How can that be controlled?
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THANK YOU VERY MUCH to all

the CCL is GREAT!

ANSWERS:

1------------------------------------------------------------------

Hi,
I'm a bit confused as to what you are asking.  If you are using periodic 
boundary conditions then when the water molecules leave one side of the 
box they just return on the other side.  When using PBC it should make no 
difference where you put the 'walls' of your box as you are hoping 
to simulate a bulk fluid.  If I am misinterpreting your question please 
let me know and I'll try to answer it again.
good luck,

Marcus Martin             Graduate Student
Department of Chemistry,  University of Minnesota
[email-masked]  http://siepmann6.chem.umn.edu/~marcus

2--------------------------------------------------------------------

It all could depend on what software you're using.

Bill Ross

3--------------------------------------------------------------------

Hi,
	PBC ensures the conserved number of particles and if it works
correctly, the leaving water will enter from the opposite side of the
box with the identical momentum. I am wondering which software are you
using.
	One important thing doing simulation with the unbalancing
chared system is the calculation of long-range interactions. For yours,
Ewald summation must not be used. Usually, I used reaction-field
method to cope with the long-range interactions if unbalance charge
is present in the box.
take care,
Noy
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3-----------------------------------------------------------------------

Hi!!

Yes, this is perfectly normal - as long as the water molecules come in
again from the opposite side.

And how could you prevent the water molecules from leaving the cell,
anyway? You would have to make the cell boundary some kind of wall,
where the molecules would be reflected. But this is exactly what you are
trying to prevent with periodic boundary conditions - namely, a finite
system that is influenced by boundary effects!

On the other hand: If you are not applying any external force to the
system, all molecules should leave the box in any direction with the
same probability. SO if you have the impression that the molecules
stream out through one side (and come in from the opposite side), then
there is something wrong with your simulation. If you want to be sure
about this, I think you should calculate the velocity auto-correlation
function of the water molecules, which has to vanish within 1ps or so.
If it does not, you are wittnessing this 'streaming effect'.

	good luck,
	gerald

Gerald Loeffler
PostDoc in Theoretical Biochemistry

EMail: [email-masked]
Phone: +43 1 79730 554
Fax:   +43 1 7987153
SMail: I.M.P. - Research Institute of Molecular Pathology
       Dr. Bohr-Gasse 7
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       AUSTRIA

4--------------------------------------------------------------------

Dear Mr Gonzalez,

what program do you use? I know this problem from SYBYL 6.1 on Sun. There it
was a bug. Within SYBYL 6.2 for Sun it is removed. But there exist other
possibilities for the observed behaviour:
1. PBC allows a few water molecules to run a bit out of the box under one
   special condition. It depends on the minimum image convention normally
   used within PBC. However, this effects only less then 5 solvent molecules
   at one simulation step (from my observations), which leave the box only up
   to a distance lower than their molecular size. In a following step they
   return to their old place inside the box or are switched to the opposite
   side inside the box, if you watch a replay of the trajectories.
2. I guess you do the simulation within an NPT ensemble. Therefore the size of
   the box must be adjustable, it changes at everey simulation step. If you
   have the box dimension frozen, but you request an NPT ensemble, then many
   programs are confused. One possible result would be like you observed.
3. The box size should be related to the NBC. NBC should be not greater than
   1/2 x boxlength. If your box is too small in relation to the NBC, it
   depends on the program how this is handled. Within SYBYL the box size will be
   enlarged without changing the number of particles, when NBC is greater
than     allowed.

Sincerely yours

B. Kallies

-----------------------------------------------------
Dr. Bernd Kallies
Institut fuer Physikalische und Theoretische Chemie
Universitaet Potsdam
Am Neuen Palais 10
14469 Potsdam
GERMANY
e-mail: [email-masked]
WWW   : http://www.chem.uni-potsdam.de/~kallies/kallies.htm
Tel   : [+49] (0)331 / 977-1313
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-----------------------------------------------------

5----------------------------------------------------------------------

I'm not sure I understand the question.

If you mean they go out one side of the cell and come in the other, then
yes that is normal.  That is why you use periodic boundary conditions.

If you mean they go out and don't come back, then no that is not normal,
and you are doing something wrong with your boundary conditions.

Have I misunderstood the question?

-------------
Visiting Research Instructor Steven J. Stuart
U.S. Naval Academy                                 
[email-masked]
572 Holloway Rd., Mail Code 9B                                  (410)
293-6636
Annapolis, MD 21402                                        fax: (410)
293-2218

6---------------------------------------------------------------------

What software are you running?  I have had similiar problems before and it
turned out that I had not defined something correctly.  If you are using
CHARMM I may be able to help.

****************************************
Troy Wymore
Department of Chemistry
University of Missouri-Columbia
Columbia, MO 65211

e-mail: [email-masked]
http://www.missouri.edu/~chemtw/troy.html
*****************************************

7--------------------------------------------------------------------------
Hi,

If you have water molecules comming in from the opposite direction, everything
is fine.

Istvan

-- 
*************************************************
Istvan Enyedy
The Catholic University of America
Chemistry Department/ Malloney Hall
Washington DC 20064
email [email-masked]
phone 202-319-5707 or 5349
fax 202-319-5381
**************************************************
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Thanks a lot ... again

			Fernando Danilo Gonzalez N.           

University of Santiago of Chile
Faculty of Chemistry and Biology         
Casilla 40, Correo 33, Santiago, Chile       fono: (562) 681 2575
E-mail : [email-masked]             fax : (562) 681 2108           
         [email-masked]
URL    : http://quimbio.usach.cl/~danilo/
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