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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