[gmx-users] protein goes out from the waterbox during MD

[Dallas B. Warren]

All that is entirely due to the PBC.  The molecule is simply no longer
centered in the box, that is all.  It is still entirely surrounded by
water.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Eugenia Polverini
> Sent: Tuesday, 30 January 2007 10:49 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] protein goes out from the waterbox during MD
> 
> 
> Dear all,
> in the output of my 5 ns MD of a small protein in a box of water and 
> pbc, I see that during MD the protein goes out from the box. 
> Why it happened? Is it a problem or I can accept that all was 
> OK? I have set the comm_mode=angular.
> 
> Thanks for your help!
> Best regards
> Eugenia
> 
> 
> 
> -- 
> Eugenia Polverini, Ph.D.
> Dept. of Physics
> University of Parma
> Parco Area delle Scienze, 7/A
> 43100 Parma
> ITALY
> 
> Phone: +39 0521 905254
> Fax: +39 0521 905223
> E-Mail: eugenia.polverini at fis.unipr.it 
> http://www.fis.unipr.it/~polveri
> 
> 
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