Jianwei Wang wrote:
Hello,
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?
Best,
Jianwei
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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
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