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

Seketoulie Keretsu sekekeretsu at gmail.com
Tue Jan 2 04:01:42 CET 2018

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. 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.
My questions are:

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

The problems seems trivial however I am unable to proceed beyond
solvation. Kindly give suggestions.

 Thank you.


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