[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Justin A. Lemkul]

On 4/27/12 6:04 AM, Anirban Ghosh wrote:
>
>
> On Fri, Apr 27, 2012 at 3:27 PM, Bala S <think_beyond at aol.com
> <mailto:think_beyond at aol.com>> wrote:
>
>     Thank you for that clarification.
>
>     I found that there were SOL molecules in .top file. I could run the EM now.
>
>     Coming to the Solvation step, I'm facing a problem.
>
>     I have made the mentioned change (0.15 to 0.375 for C) in the vdwradii.dat
>     locally.
>
>     While adding the solvent molecules, what command should I be using?
>
>     I am using the usual command I use for non-membrane simulations,
>
>     $ editconf -f shrinked4.gro -o shrinked4_1.gro -c -d 1 -bt cubic
>
>     followed by
>
>     $ genbox -cp shrinked4_1.gro -cs -o shrinked4_box.gro -p topol.top
>
>
> When you mention -bt cubic, it adds a cubic water box all around your system (if
> you visualize you will see your entire bilayer immersed in a cubic water box
> like a normal protein solvation). But that is wrong. You need to add water only
> on either side of the lipid membrane (that is along the z-axis only). So use the
> -box option with editconf without using -c and -d. You can have a look at
> https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial It is clearly
> mentioned over there how to go about it.
>
>

You should not add water in between InflateGRO steps.  The process should be 
carried out entirely in the absence of water, otherwise you add solvent to a 
huge box and the water is incorporated into the voids in the lipid membrane. 
Only after the last shrinking step should you proceed with adding water.

-Justin

>     calculation goes for long time showing a huge number of SOL molecules.
>
>     I guess I'm worng somehere.
>
>     Thanks.
>
>     Bala S
>
>
>
>
>
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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