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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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