[gmx-users] bondtype 5

Nicolas Schmidt nicolas-schmidt at gmx.de
Thu May 17 22:38:09 CEST 2007

This may be a really simple question, I know, but still...

How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwards):

WARNING 1 [file "ethane.itp", line 12]:
  No default Connect Bonds types, using zeroes

Either way I'm not sure how the distance of these two atoms is processed, so there is NO parameter that is specifying this bond-type (and a constraint would be processed by gromacs, wouldn't it? And I don't want it to, cause I want the simulation to be as simple as possible)

By the way, I wanna simulate a huge system of ethane and take a look at the processing time per simulated step, is there an output-file thats reading this?

Thanks in advance to everyone who is replying, it's so hard when you're stuck. 
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