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

[Anirban Ghosh]

On Fri, Apr 27, 2012 at 3:27 PM, Bala S <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.


>
> calculation goes for long time showing a huge number of SOL molecules.
>
> I guess I'm worng somehere.
>
> Thanks.
>
> Bala S
>
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933479.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120427/cd876db4/attachment.html>