[gmx-users] About cutt-off scheme ..

rama david ramadavidgroup at gmail.com
Thu Mar 29 13:11:06 CEST 2012

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 *.
    *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??
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