[gmx-users] [Fwd: Semiisotropic pressure coupling &comm_grps (VCM)]

[Alok]

Dear Xavier,

Thanks a lot for your reply. I will follow  your suggestions.

Best Regards,
Alok
----- Original Message ----- 
From: "Xavier Periole" <X.Periole at rug.nl>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, November 26, 2007 5:23 PM
Subject: Re: [gmx-users] [Fwd: Semiisotropic pressure coupling &comm_grps 
(VCM)]



> I have two basic questions regarding membrane protein simulation. First
> regarding Semiisotropic pressure coupling (NPAT) and second regarding
> comm_grpp (VCM).
>
> 1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be
> fixed) then is following the correct way to define?
>
> Pcoupl                   =  Berendsen
> Pcoupltype            =  semiisotropic
> tau_p                     =   2.0     2.0
> compressibility     =   0        4.5e-5
> ref_p                     =  1.0      1.0
>
> In some of the previous mails on same topic ref_p was defined as 0.0
> 1.0 in place of 1.0   1.0 even they was using compressibility 0.0
> 4.5e-5, that's why I am confuse. Do I have to take ref_p = 1.0   1.0 or
>  0.0   1.0 when I am using compressibility 0.0   4.5e-5 (NPAT). I think
> if I am taking compressibility value 0 then it doesn't matter what value
> I have taken for ref_p, but I want to confirm it.

I would guess that ref_p = 1.0 1.0 and ref_p = 0.0 1.0 would give
the result since you define compressibility = 0.0 4.5e-05

you can check that by running small trajectories ...

> 2) I want to remove center of mass translation so in following which one
> is better?
>
>     a)    comm_mode                =  Linear
>            nstcomm                       =  1
>            comm_grps                  =  Protein_POP ; (both protein and
> lipid are together)
>
>     b)    comm_mode                =  Linear
>            nstcomm                       =  1
>            comm_grps                  =  Protein POP ; (protein and
> lipid separately)

It is better to remove the COM of both bilayer (plus protein) and the
aqueous phase:
comm_grps = Protein_POP SOL

XAvier

>
>
> Thanks a lot
>
> Best Regards,
> Alok
>
> -- 
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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