On 11/5/12 8:20 AM, vidhya sankar wrote:
Dear Justin ,
Thank you for your Previous reply
I am following your Protein Lipid Tutorial
After Several Shrinking and several EM of my system i reached the APL for
DPPC 64am^2
, I Have Added the ions to Neutralize the system . Then I have Done EM When I
Visualize The system in VMD
it was good As in the tutorial Web page
Then I did NVT Equilibration , when i see the Resultant .gro file in VMD All
the Lipid Molecules are just away from the protein ( which is Kept in center
of Box)
While some of the Water Molecules are nearer to Protein ( it means that during
Equilibration water molecules are diffusing towards protein while Lipid
Molecules are Diffusing Away from Protein Which is in the center) Is it
correct or Wrong ?
Where I have committed the Mistake ? Is my System Contains Voids ?
Also Tail part of the Lipid molecules are protruding outside Box While Head
part is in the Solvent Region (it means some Lipid Molecules Are flipped up)
I have no idea what has gone wrong. It sounds like whatever you've done to
build the system was incorrect.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
