[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:
> 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 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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