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
1.0
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 ???
or
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:
http://lists.gromacs.org/pipermail/gmx-users/2012-March/069617.html
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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