-------- Original Message --------
Subject: Semiisotropic pressure coupling & comm_grps (VCM)
Date: Mon, 26 Nov 2007 13:04:05 +0530
From: Alok <[EMAIL PROTECTED]>
To: <[EMAIL PROTECTED]>
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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