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

Bala S think_beyond at aol.com
Fri Apr 27 11:57:48 CEST 2012

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

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

calculation goes for long time showing a huge number of SOL molecules.

I guess I'm worng somehere.


Bala S

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