[gmx-developers] trjconv and -pbc whole option

David Bostick dbostick at scripps.edu
Sun Oct 30 02:22:54 CET 2005

Hello all,

I ran into something with trjconv that is confusing me and I wanted to be 
sure I was correct in my thinking before submitting a bug report.  I tried 
centering a configuration with trjconv along with the -pbc whole option.  
It was my understanding that -pbc whole should produce whole molecules, 
however after centering a configuration using :

-center rect -pbc whole

I found truncated water molecules at the edges of the box.  I think there 
must be something wrong.  Am I right?  If the -pbc whole option is 
supposed to make all molecules in the box whole after wrapping the 
coordinates due to pbcs, has anyone else had this problem?

Thanks in advance,


David Bostick			       |
The Scripps Research Institute         |
Dept. of Molecular Biology, TPC 6      |
10550 N. Torrey Pines Rd. 	       |
La Jolla, CA 92037		       |	
Phone: 858-784-9614		       |
Fax:   858-784-8688		       |
Email: dbostick at scripps.edu	       |
Web:   http://www.scripps.edu/~dbostick|

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