On 4/27/12 6:04 AM, Anirban Ghosh wrote:


On Fri, Apr 27, 2012 at 3:27 PM, Bala S <think_bey...@aol.com
<mailto:think_bey...@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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