[gmx-users] shift functions in gromacs
pavkudr at gmail.com
Sat Jul 23 14:39:38 CEST 2011
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
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,
More information about the gromacs.org_gmx-users