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

[David van der Spoel]

-------- Original Message --------
Subject: 	Semiisotropic pressure coupling & comm_grps (VCM)
Date: 	Mon, 26 Nov 2007 13:04:05 +0530
From: 	Alok <alokjain at iitk.ac.in>
To: 	<spoel at xray.bmc.uu.se>



Dear Sir,

Sorry for personnel mail. I have posted these question in gromacs
mailing list but I haven't got the answer. So I am sending you personally.

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.

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)


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