[gmx-users] [pairs] section

David spoel at xray.bmc.uu.se
Thu May 27 19:54:41 CEST 2004

On Wed, 2004-05-26 at 17:38, Nuno R. L. Ferreira wrote:
> Hi *
> Just to put my ideas in order.
> When writing an .itp file for a molecule, say a phospholipid, if the 1-4 
> non-bonded interactions are already explicitly defined under *nb.itp, then it 
> is not necessary to write again those interactions under [pairs] section of 
> this phospholipid .itp.
> Is this correct?

check the section on pairs and exclusions in the manual (chap 4).
everything that's not excluded gets full nonbondeds. the rest gets only
what you define. note the difference between the xxx-types parts of the
topology and the corresponding xxx sections. (see chap 5).
> Best regards,
> Nuno
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://xray.bmc.uu.se/~spoel

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