[gmx-users] using implicit water for atomistic simulation of lipid bilayer

[Mohsen Ramezanpour]

Dear Gromacs Users,

I was wondering if there is any example of using Implicit water model for
lipid bilayers in Gromacs?

I have read on using implicit solvents in Gromacs and found interesting
discussions:

https://groups.google.com/forum/#!topic/archive-gmx-users/0HIFVop390I

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-December/066830.html


As I understood, using implicit solvent assumes an infinite solvent around
the solute.

Which seems good for peptide/protein folding. I did not see any example for
bilayers.

Assuming that implicit solvent is well parameterized to work with lipid
membranes, the one problem seems to be the PBC option in mdp file.

PBC = no is appropriate for using implicit solvent while PBC = xyz is the
usual case for bilayers.

Is there any way to split the PBC treatment for water and bilayer? Like
what we do in T-coupling for different groups.

Also, I want to mix this implicit solvent with atomistic force field, like
Gromos FF, not MARTINI.

Thanks in advance for your comments.

Cheers,
Mohsen

-- 
*Rewards work better than punishment ...*