Manohar Murthi wrote:
karim
trust is good.
one possible method to generate your initial
configuration is to do monte carlo insertions of
solvent molecules until the desired numbers of
each are present in your box. this method
has the advantage that the box will be truly mixed.
there are probably many codes out there to do this,
but i use music by the snurr research group
(http://zeolites.cqe.northwestern.edu), which
allows you to stop a grand canonical monte carlo
sim (constant mu,v,t) when user-defined criteria
have been met.
if you choose to use this method, be warned that
you'll have to do a really thorough energy
minimization before launching your md.
cheers
mo
I'd say use MD. Put N methanol in a box, put M water in another box.
Translate methanol (using editconf)
merge boxes using emacs
run md with pressure coupling.
done.
--- [EMAIL PROTECTED] wrote:
Message: 5
Date: Thu, 27 Apr 2006 11:03:03 +0430
From: "Mahnam" <[EMAIL PROTECTED]>
Subject: [gmx-users] Mix solvent
To: [email protected]
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain
In God We Trust
Hello GMX users
I want to use gromacs program to study a protein in
a solvent of the mixture
of 30% methanol and 70% water. Would you please
tell me how can I make gro
file of "mix solvent" box for genbox.
Thank you very much in advance
Karim Mahnam
Institute of Biochemistry and Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/
------------------------------
Message: 6
Date: Thu, 27 Apr 2006 18:30:38 +1000 (EST)
From: "Mark Abraham" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Mix solvent
To: "Discussion list for GROMACS users"
<[email protected]>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain;charset=iso-8859-1
In God We Trust
Hello GMX users
I want to use gromacs program to study a protein
in a solvent of the
mixture
of 30% methanol and 70% water. Would you please
tell me how can I make
gro
file of "mix solvent" box for genbox.
There's no straightforward approach that I'm aware
of. One possibility is
to do the arithmetic for the size box you want to
use and generate a
smaller box filled with N water molecules that will
give you 70% were you
to increase the size of the box and fill the gaps
with methanol. Then
increase the size of the box, and use the -nmol and
-ci options to genbox
to add enough methanols to make the mix 70/30. Then
you will need to
equilibrate that box for a while to get a good mix
of solvents at
reasonable density and pressure. I think you should
be able to use that
box later for subsequently doing genbox for your
protein.
You could also manually delete enough waters to get
down to 70%, and use
the genbox options above to try to fill the gaps,
but you will have a hard
time fitting methanol into water-sized holes.
Mark
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________________________________________________________________________
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