Dear gmx-users (and developers ;-) I believe there are false LJ pair-parameters in gromacs' implementation of the GROMOS 45a3 force field for interactions between the atoms of DMSO, and between the atoms of chloroform. The C6/C12 pair paramteters for CDMSO-SDMSO, ODMSO-SDMSO, ODMSO-CDMSO, and CLCHL-CCHL, HCHL-CCHL, HCHL-CLCHL in ffG45a3nb.itp are simply the (root of the) product of the individual atomic parameters, whereas separate parameters - with no relation to the atomic ones - are defined in the original GROMOS force field. The errors are there in the force field files distributed with gromacs version 4.0.5 all the way down to at least version 3.2.1 (it's as far as I've looked), and also in the ffG45a3.tar.gz file to be found at http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields
For example: The lines in ffG45a3nb.itp read: CDMSO SDMSO 1 0.009777435 2.1627421e-05 ... ODMSO SDMSO 1 0.004897196 4.0192831e-06 ODMSO CDMSO 1 0.0045335636 4.0434685e-06 However, they should be CDMSO SDMSO 1 0.0097827 2.16523e-05 ... ODMSO SDMSO 1 0.0052442 4.6094e-06 ODMSO CDMSO 1 0.0049187 4.7597e-06 as they are in the GROMOS 43a1 force field. A similar problem holds for chloroform (atoms CCHL, CLCHL and HCHL). Find attached a corrected version of ffG45a3nb.itp. Cheers, Roman -- ======================================= Roman Affentranger, Ph.D. Group of Computational Biology and Proteomics Institute of Biotechnology and Biomedicine Universitat Autònoma de Barcelona E-08193 Bellaterra (Barcelona) Phone: (+34)93 581 2807 Fax: (+34)93 581 2011 E-mail: roman.affentran...@bioinf.uab.es =======================================
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