[gmx-users] confirming behavior in cases of no default XXX types...

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 24 21:30:44 CEST 2006

David Mobley wrote:
> All,
> I am trying to set up some relative free energy calculations where,
> for example, I mutate one residue into another residue. Anyway, I just
> need to confirm something about the warnings GROMACS issues about "No
> default Bond types, using zeroes", etc.
> In particular, when GROMACS finds no such parameters for the A state
> and uses zeroes, does it still look for B state parameters and, if
> found, use nonzero parameters for these? This is what I would LIKE,
> but I want to confirm that it's what's going on.

you can check this by gmxdump, it's not very user-friendly but there 
you'll find what grompp makes of your input.

> Thanks,
> David
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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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