* Borys Szefczyk <[email protected]> [2009-06-07 14:12:14 +0200]:
On Sat, Jun 06, 2009 at 02:06:56PM +0200, Florian Dommert wrote:* David van der Spoel <[email protected]> [2009-06-06 08:06:26 +0200]:The VDW may work, but not differently scaled 1-4 and 1-5 coulomb interactions.Where is the matter if I have a [ pairs ] directive in the itp file like this :[ pairs ] ; ai aj fu 1 5 2 0.5 -0.11 0.13 0.30250 0.095865 1 6 2 0.5 -0.11 0.13 0.30250 0.095865 . . . .;this is are nonbonded intramolecular IAs separated by more than theree bonds2 5 2 7.569 0.07200 0.02300 0.00000 0.00000 2 6 2 7.569 0.07200 0.02300 0.00000 0.00000I think this will work, but setting LJ parameters to zero will cancel the interaction for these pairs. Is this what you intend to do?
Glad to hear the my help works. Setting the LJ parameters zero for the should avoid a further contribution of the LJ part from the defined 1-5 IA, since they are already present in the nonbonded part of the interaction types. Accoring to Chapter 5.3.4 of the manual, the [ pairs ] directive allows to add further nonbonded energy terms within a molecule. This is exactly the goal we want to achieve ;) Cheers, Flo
I did a simple test: I've defined an abstract molecule like this: X-X-X-X-X so that 1 and fourth atom are 0.4 nm apart, and 1 and fifth atom are 0.5 nm apart. I've set all bonded and non-bonded interactions to zero, Nexcl=3, gen-pairs=yes, fudgeQQ=1.0, fugdeLJ=1.0. Then I have defined [pairs] like this: [ pairs ] 1 4 2 1.0 0.1 0.0215927 0.325052 0.25 1 5 2 1.0 0.1 0.0287903 0.433402 0.25 charges, sigma and epsilon are chosen in such a way that each interaction should contribute exactly 1 kJ/mol. Indeed, the potential energy calculated by GROMACS is 4 kJ/mol. Now, changing the pairs to: [ pairs ] 1 4 2 0.5 0.1 0.0215927 0.325052 0.25 1 5 2 0.8 0.1 0.0287903 0.433402 0.25 I get the potential energy of 3.3 kJ/mol, which means that coulomb14 whas rescaled from 1 to 0.5 and coulomb15 was rescaled from 1 to 0.8. This is exaclty what I was looking for. Thanks for all the comments, Borys -- REQUIMTE, & Molecular Modelling & Quantum Chemistry Group, Department of Chemistry, & Institute of Physical & Theoretical Chemistry, Faculty of Science, & Wroclaw University of Technology University of Porto & http://ichfit.ch.pwr.wroc.pl/people/szefczyk _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected].Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Tel: +49 - 711 / 6856-3613 Fax: +49 - 711 / 6856-3658 EMail: [email protected] Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert !! PGP-ENCODED emails preferred !!
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