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