Re: REG Protein inserion in to membrane bi layear

From: Vermaas, Joshua (
Date: Thu Jun 22 2017 - 12:25:00 CDT

Hi Arthur,

I feel like this problem is pretty tricky. Have you tried the reverse
process (extracting an embedded protein from a membrane), and estimated
the rough timescales required from the diffusivity along the extraction
reaction coordinate and the pmf? My money is on this process being so
slow (a timescale of minutes or hours or longer!) that even CG isn't
fast enough to see the process spontaneously.


On 06/22/2017 09:28 AM, Arthur Oliveira Vale wrote:
> Dear Joshua Vermaas,
> Thank you for the prompt reply! After re-checking constantRatio we also think that constant ratio will be fine. We were indeed thinking about coarse-graining due to the larger timescale for lipid diffusion in bilayers. We have only done all-atom simulations before, and therefore I would like to elicit some tips about it if possible. What we were thinking was to use a coarse-grain model for the lipids, but keep the rest all-atoms (keeping water as all-atom is relevant because we would like to analyze water diffusion in the protein pore). Do you think this is reasonable?
> Also, we are under the impression that MARTINI is considered a good forcefield for coarse-grained lipids, is that what you would suggest we use?
> Thank you once again for the help!
> Arthur Vale
> ________________________________________
> From: Vermaas, Joshua []
> Sent: Tuesday, June 20, 2017 10:49 AM
> To:; Arthur Oliveira Vale
> Subject: Re: namd-l: REG Protein inserion in to membrane bi layear
> Could you be clearer as to what your question is? PBC options are the same as ever: make a box big enough to contain your system. If you use a barostat, make sure the flexiblecell and constantratio options are turned on, since this is still a membrane-embedded system. This doesn't change if your protein is above the membrane or embedded in it.
> -Josh
> On 06/20/2017 04:17 AM, Vidhya Sankar wrote:
> Respected sir
> I am doing simulation for insertion of Protein kept above the membrane along Z axis through all atom atomistic simulation
> In My Configuration file
> How to set Periodic boundary condition for my system normally in tutorial Protein packed inside membrane . But My case have protein kept above membrane
> Any other way to set cell basis vector ?
> I request your valuable suggestion
> With Cheers
> S.Vidhya sankar

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