1. Are the other membrane protein simulations available. Perhaps more comprehensive ones?

Nothing more than Dr. Lemkul's tutorial. Its best.

2. After changing the value of C to 0.375 in the vdwradii.dat file at the working directory, should i copy the vdwradii.dat to /home/..../gromacs/top directory (where the file was originally located)?

Yes, its ok if you do. But I guess it works without copying as well.

3. The tutorial mentioned " Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide." I am unable to locate 'GMXLIB'. Does GMXLIB refer to the directory in which the forcefield files (eg. ffnonbonded.ipt) were located or should i create a GMXLIB directory.

Yes, where forcefield files are located.

Please see my reply on gmx-users. You're adding steps that don't exist.

For future reference: The problem encountered resulted due to two reasons

1. I failed to run the inflategro 26 times (or as many as required to shrink the system). Corrected by executing the inflategro 26 times and minimizing system after each iteration.

2. During solvation step, i used the protein_ ligand simulation tutorial as a reference and set "-bt dodecahedron" , "-d 1.0" etc. This should not be done.

Dear, Dr, Justin, Please can you guide guide me how to calculate diffusion coefficient through gmx analysis program. Though, I have searched your answers in mail archive but I failed to find any helpful guide. Please help if possible.

Dear Khair, use gmx msd tool to calculate the diffusion coefficient.

Nr. 3

$GMXLIB and any other that starts with $ sign (like $PATH for example) in linux is a variable. You can print it using:

echo $GMXLIB

You can set it like (although you should not mess around with the default settings):

GMXLIB="The path to the directory that you want"

This means that the $GMXLIB is not a folder named GMXLIB, this is why you can't find it. If you echo-it you will see the actual name and path to the folder that is being used.

Advice:

Look up periodic boundary conditions (PBC) and you will understand why are some parts of your system "outside" the box. This is not a problem, in fact they are not even outside the box because your box repeats itself in each direction (x, y, z) so what comes out on the right goes back in on the left, and so on. The software is visualizing it this way, so you can see the molecule as one piece instead of broken fragments. Wherever you have a part "outside" you should check for a similar shaped "hole" on the opposite side.

This is true for every box type but it's easier to see it with a cube shaped one in cartesian coordinates.

Thank you so much Roshan Shrestha and Csongor Matyas for your cooperation.