[gmx-users] How to turn 1-3 interactions on?
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 1 22:13:55 CEST 2006
Jianwei Wang wrote:
> This has something to do with exclusion list.
> I have a special need and have to turn 1-3 interactions on, that is, I
> need nobonded interactions (vwd and electrostatic) included in energy
> calculations for atoms more than one bond away. I have tried the
> following, seems gmx still excludes 1-3 interactions because I have atom
> close contacts (less than 0.1 Angstroms)and like-charged atoms looking to
> each other, and my system stalls:
> (1) assign nrexcl with 1 in [ moleculetype ]
this is the correct way. do also turn off the pairs ( I assume you need
full 1-4 as well).
use gmxdump -s topol.tpr | less to check your tpr. From within less you
can search for excl which is the list of exclusions. It shoul donly
contain the bonds now.
> (2) all bonds use function type 6
> (3) what else?
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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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