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

[Mark Abraham]

Hi,

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

> 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
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


> 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?

Mark


> The problems seems trivial however I am unable to proceed beyond
> solvation. Kindly give suggestions.
>
>  Thank you.
>
>
> Sincerely,
> Seke
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>