[gmx-developers] trjconv and -pbc whole option

[David Bostick]

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

-- 
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David Bostick			       |
The Scripps Research Institute         |
Dept. of Molecular Biology, TPC 6      |
10550 N. Torrey Pines Rd. 	       |
La Jolla, CA 92037		       |	
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