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

[Dallas Warren]

http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 29 Aug 2019 at 14:35, Muthusankar <muthubioinf at gmail.com> wrote:

> 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
> --
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