[gmx-users] KALP15 in DPPC: Bilayer out of solvation box

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 2 06:52:59 CET 2018


On Tue, Jan 2, 2018 at 3:02 AM Seketoulie Keretsu <sekekeretsu at gmail.com>

> Dear Experts
> I am currently doing the gromacs tutorial for simulation of membrane
> protein (KALP15 in DPPC by Justin A. Lemkul). I came across several
> challenges most of which I could resolve. However, the result after
> solvation wasn't as expected. That is, a small portion of the DPPC
> bilayer was out of the solvation box and also the the water was no
> distributed over the system as mentioned in tutorial (or atleast it
> wasn't observable in VMD). I have done just as in the tutorial. I have
> no clue why the bilayer went outside the solvation box since i
> followed and executed just as mentioned in the tutorial.

This just seems like normal consequences of a simulation using periodic
boundary conditions that are then visualized without considering those
consequences... see

> I suspect the
> later issue, that is, the distribution of water all over the system
> could be due to the step in which the changing of the value of C from
> 0.15 to 0.375 in vdwradii.dat wasn't effective.

Why do you think that? Did you compare with leaving the value unmodified?

> My questions are:
> 1. Are the other membrane protein simulation tutorials available.
> Perhaps more comprehensive ones?

Justin's tutorials are of very high quality and rather comprehensive.

> 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)?

You should do whatever the tutorial suggests. In practice, both work the
same. Being able to leave the modified file in the working directory is
convenient in multiple ways.

> 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.

GMXLIB is an environment variable that is set up when you run "source
/path/to/GMXRC" that helps the tools find the databases in
/path/to/gromacs/share/top. You could put the directory there, or leave it
in your working directory, whatever is more useful and convenient for you.
Do you plan to use it again?


> The problems seems trivial however I am unable to proceed beyond
> solvation. Kindly give suggestions.
>  Thank you.
> Sincerely,
> Seke
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