Hi, I am sure that this is a rather basic question, but I am wondering if you can please help me to understand something described in the manual.
What is the purpose of the [ pairs ] section of an .itp file? What information does it contain? Section 5.3.4 (page 112) of the version 4.5.4 manual says: "Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [ pairs ] section of a molecule definition. The parameters for these interactions can be set independently from the non-bonded interaction parameters. In the GROMOS force fields, pairs are only used to modify the 1-4 interactions (interactions of atoms separated by three bonds). In these force fields the 1-4 interactions are excluded from the non-bonded interactions (see sec. 5.4)." However, I am using the OPLS force field, not GROMOS. OPLS prescribes that 1-4 nonbonded interactions are to be taken at half strength (i.e., fudgeQQ = 0.5 and fudgeLJ = 0.5). Does this mean that I should specify all possible 1-4 nonbonded interactions in the [ pairs ] section? If I have nrexcl = 3 specified in [ moleculetype ], then can I assume that 1-5, 1-6, 1-7, etc, interactions will be taken into account (at full strength), even if such pairs are not specified in [ pairs ]? I have set gen-pairs = yes, fudgeLJ = 0.5, and fudgeQQ = 0.5. Thank you for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
