[gmx-users] bondtype 5

David van der Spoel spoel at xray.bmc.uu.se
Thu May 17 22:47:32 CEST 2007

Nicolas Schmidt wrote:
> 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. 
[ constraint ]
; i j type length
1 2 1 0.15

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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