[gmx-users] About cutt-off scheme ..
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 29 13:35:32 CEST 2012
rama david wrote:
> Hi Gromacs users ,
> as per the link given on gromacs website...
> Introduction to Molecular Dynamics Simulations and Analysis
> <http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/> - Tutorial for
> performing and analyzing simulations of proteins. Includes examples of
> many of the gromacs analysis tools and addresses a number of issues that
> are commonly raised on the GROMACS user list. This tutorial uses GROMACS
> version 3.3.1 (Tsjerk A. Wassenaar).
> editconf -f protein-EM-vacuum.pdb -o protein-PBC.gro -bt dodecahedron -d
> mdp file parameter are as follow ,
> coulombtype = Reaction-Field
> rcoulomb = 1.4
> epsilon_rf = 78
> epsilon_r = 1
> vdw-type = Cut-off
> rvdw = 1.4
> so my query is ..
> As mention in manual ...
> (Page no 14 manual 4.5.4 I am using the Gromacs 4.5.4 )
> *This means that the length of each box vector must exceed the length of
> the macromolecule in the
> direction of that edge plus two times the cut-off radius Rc *.
Read the next sentence in the manual.
> /In the tutorial -d 1.0 is less than 1.4 ./..
> I noticed that manual version and tutorial gromacs version are
> different ...
> But it raise a lot of confusion for new users like me..
> 1. Is the -d .. should be equal or more than cutt off ???
> Is the -d .. should be equal or more than cutt-off??
The basic point is that in all simulations you have to avoid the same molecule
"seeing" itself across a periodic boundary. So in reality, you need a periodic
distance (which is equivalent to the value set with -d, times 2) that exceeds
the longest cutoff. Assuming the unit cell does not undergo massive shrinking,
this value is generally pretty stable in an aqueous environment. Setting -d 1.0
is common because it creates a 2.0-nm distance between a centered solute, which
exceeds your cutoff and is sufficient to avoid the influence of water ordering,
as discussed recently:
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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