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

[Justin Lemkul]

On 1/1/18 10:01 PM, Seketoulie Keretsu 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. 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.

I see from your RG post 
(https://www.researchgate.net/post/Gromacs_tutorial_preparation_and_simulation_of_a_simple_membrane_protein_available) 
that you are solvating during the InflateGRO steps. The tutorial does 
not tell you to do that, so don't. All of those minimizations should be 
carried out in vacuo.

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

What would you define as "more comprehensive" that would be more useful?

Note that my tutorial warns that it is advanced and users are expected 
to understand lots of routine things that I don't explicitly say in the 
tutorial. If there are elements that are unclear, then I'm happy to hear 
about them. It's been online for about 9 years now, and my email has 
significantly tapered off, so I'm assuming most issues have been 
resolved over time, but if that's not the case, feedback is always welcome.

> 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)?

No, because then your increased C radius is globally applied to every 
system you work with, which won't be appropriate.

-Justin
> 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.
>
>
> Sincerely,
> Seke

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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