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

[Mohsen Ramezanpour]

Thanks Justin.

Agreed. I wanted to make sure about that.

Cheers

On Sat, Dec 10, 2016 at 12:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/9/16 5:58 PM, Mohsen Ramezanpour wrote:
>
>> 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.
>>
>>
> I don't think GROMACS (or any other program) can handle this.  Perhaps you
> can get CHARMM to do it via the GBMW module, but even that (I'm pretty
> sure) requires an implicit bilayer (e.g. layers of high and low dielectric
> constant only, no mixture of explicit + implicit).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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