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