[gmx-users] Mix solvent
David van der Spoel
spoel at xray.bmc.uu.se
Thu Apr 27 16:10:29 CEST 2006
Manohar Murthi wrote:
> 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.
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.
> --- 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
>> <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
>> 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>
> <354126.96.36.199.225.1146126638.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
>>> of 30% methanol and 70% water. Would you please
>> tell me how can I make
>>> 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
>> 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.
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> End of gmx-users Digest, Vol 24, Issue 90
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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