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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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