[gmx-users] Why protein structure is outside of lipid environment after MD simulation using Gromacs?

[Muthusankar]

Can anyone guide me,
First time, I run the program of MD simulation of Membrane environment
using gromacs software.
My protein is an integral membrane protein. First, I have prepared the
protein.PDB using OPM server and CHARMM-GUI (SDPC lipid bi-layer) membrane
builder. Then I have run MD simulation by gromacs software. I have
visualized equilibration output file and the protein structure was properly
fit with lipid environment. Then I run the program of MD production at
10ns, I got the output file of .gro. I have converted .gro into .pdb file
and visualize the pymol software. The protein structure is outside of the
lipid environment (far away). I don't know how to fix the problem.

-- 
With regards
*Dr. Muthu Sankar Aathi*
*ICMR Post-Doctoral Fellow (ICMR-PDF),*
Biomedical Informatics Centre,
ICMR-National Institute for Research in Reproductive Health (NIRRH),
Parel, Mumbai-400 012, India.

Email: muthubioinf at gmail.c <muthubioinf at gmail.com>om
Mobile No.  +91 9080444540