[gmx-users] Mix solvent

[Manohar Murthi]

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

--- gmx-users-request at gromacs.org wrote:

> Message: 5
> Date: Thu, 27 Apr 2006 11:03:03 +0430
> From: "Mahnam" <mahnam at ibb.ut.ac.ir>
> Subject: [gmx-users] Mix solvent
> To: gmx-users at gromacs.org
> Message-ID:
> <WorldClient-F200604271103.AA03030004 at ibb.ut.ac.ir>
> 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" <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] Mix solvent
> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Message-ID:
> 
>
<35477.150.203.7.225.1146126638.squirrel at sqmail.anu.edu.au>
> 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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> End of gmx-users Digest, Vol 24, Issue 90
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