[gmx-users] About EM for Lipid Protein Tutorila

Justin Lemkul jalemkul at vt.edu
Thu Oct 18 17:30:52 CEST 2012

On 10/18/12 11:07 AM, vidhya sankar wrote:
> Dear Justin Sorry   for the inconvenience in the previous Mail .
> I am Much obliged for your  Previous help
> Now I  am following Your Lipid Protein Tutorial
>   I am using DPPC128.pdb And I Have Downloaded the DPPC.itp and topol_DPPC.top When I run the energy Minimization (em.mdp Downloded form your  website) for the this Lipid I have got Following error
> Warning: 1-4 interaction between 1256 and 1259 at distance 3.831 which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>   I am using Default .itp , .top (Down Loaded from website quoted by you)  and Dppc.gro (created by Editconf tool)
> Why this error comes ?
> I Have not manually constructed  .top for lipids May be there are several discussion about this error in Mailing Archive .
> Here You Have not mentioned this type of error in your website  Where have i committed Mistake?

You should not see such errors if you follow the tutorial exactly.  Note that 
the required dppc128.gro file is not simply created by editconf, its periodicity 
must be accounted for using trjconv.  If you have skipped this step in the 
tutorial, the lipids will be broken and the coordinate file useless.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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