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

[Justin A. Lemkul]

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

-- 
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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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