[gmx-users] shift functions in gromacs

Павел Кудрявцев pavkudr at gmail.com
Sat Jul 23 14:39:38 CEST 2011

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,

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