Hello everyone, I'd like to ask for some clarification of actual form of shift fuctions used in gromacs. Due to gromacs tutorial 4.5.4 (section 4.1.5) and equations 4.23, 4.26-4.31 shift fuction seems to depend only on 2 user-defined conctants - r1 and rc which seems to be rvdw_switch and rvdw respectively. Nevertheless in section 7.3.11 declared that using of VdW type Shift decrease LJ potential over the whole range regardless of rvdw_switch and only forces depends on both rvdw_switch and rvdw. Such behaviour seems to be ok if take into account next words from section 4.1.5 "When r1 = 0 this is a traditional shift function,otherwise it acts as a switch function" but it does not fit given aquations because then there must third constant besides r1=0 and rc.
One more question: several times I saw in articles people using short VdW cut-off like 8 A with Amber force fields (for example recent article "Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins" DOI: 10.1021/ct200094b), but they dont say anything about trucation type. Does it mean there is some kind of standart parameters set for such small cut-off or is it ok to use it without shifting/switching? thanks in advance, Pavel -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
