[gmx-users] Re: Updating to 3.3 version...

[Absalom Zamorano]

Hi everyone, I have the version 3.2.1, but now I want
to update it with the version 3.3, How can I uninstall
the 3.2.1? is it mandatory?, I will apprecite it very
much some guide about it.
Thanks for advance...
 --- gmx-users-request at gromacs.org escribió:

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> Today's Topics:
> 
>    1. Re: Locally Enhanced Sampling
> (msonoda at iqm.unicamp.br)
>    2. Re: genion error (Yang Ye)
>    3. Re: Locally Enhanced Sampling (David van der
> Spoel)
>    4. altLoc (Tamas Horvath)
>    5. Re: altLoc (David van der Spoel)
>    6. Re: altLoc (Tamas Horvath)
>    7. glycosylated residues (Lars Meinhold)
> 
> 
>
----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 16 Jan 2006 08:56:32 -0200 (BRST)
> From: msonoda at iqm.unicamp.br
> Subject: Re: [gmx-users] Locally Enhanced Sampling
> To: "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Message-ID:
> 
>
<43219.143.107.228.50.1137408992.squirrel at pcserver.iqm.unicamp.br>
> Content-Type: text/plain;charset=iso-8859-1
> 
> > Ran Friedman wrote:
> >> Hi,
> >>
> >> You're probably better off with moil.
> >>
> > That does seem to have it implemented.
> >
> > Naive question: what does the algorithm do?
> 
> 
> Locally Enhance Sampling was initially
> proposed by Elber and Karplus
> (jacs, (1990) 112:9161) to study
> carbon monoxide escaping through
> myoglobin. To improve sampling,
> many copies of a small part of
> the system (eg CO) are made,
> where the copies DO NOT interact
> each other, the interaction between
> the copies and the large part
> of the system (eg myoglobin)
> is scaled by the number of copies.
> In this way, the energy barrier
> that CO must overcome to scape is
> decreased, and the probability of
> observation of a scape is increased
> exponentially.
> 
> Many theoretical improvements in the
> method has been done by Ulitsky, Elber,
> Straub and Karplus
> (JCP (1993) 98:3380; JCP (1991) 94:6737;
> JPC (1994) 98:1034).
> Basically, they wanted to map the
> dynamics of each copy to the dynamics
> observed if there were not copies
> (ie one single CO) in order to observe
> correct time dependent properties.
> 
> 
> >
> >> Ran.
> >>
> >> Alexandre Suman de Araujo wrote:
> >>
> >>> Hi Gmxers!
> >>>
> >>> I´d like to perform some Locally Enhanced
> Sampling (LES) simulations
> >>> of a ligand in a protein and I´d like to know if
> it´s possible with
> >>> Gromacs and, if yes, what I need to do to
> implement this kind of
> >>> simulations.
> >>> Thanks!
> >>>
> >>
> >>
> >
> >
> > --
> > David.
> >
>
________________________________________________________________________
> > 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://xray.bmc.uu.se/~spoel
> >
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 16 Jan 2006 20:15:16 +0800
> From: Yang Ye <leafyoung81-group at yahoo.com>
> Subject: Re: [gmx-users] genion error
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <43CB8E54.1070206 at yahoo.com>
> Content-Type: text/plain; charset=ISO-8859-1;
> format=flowed
> 
> As a repeating theme of this list, again, it is not
> recommended to only 
> couple a few atoms. Just use two groups: Protein and
> Rest for t-coupling.
> 
> bharat at sscu.iisc.ernet.in wrote:
> >> Please let me know what values of ref_t and tau_t
> is appropriate for
> >> this calculation. And any other points to
> correct.
> >
> > i think, u have to use one more column telling
> ref_t and tau_t for 
> > ions, as shown below
> >
> > ref_t               =3D  300 300 300
> > tau_t               =3D  0.1 0.1 0.1
> >
> >
> > bharat
> > _______________________________________________
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> 
> -- 
> /Regards,/
> Yang Ye
> /Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884
> /
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 16 Jan 2006 13:40:10 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Locally Enhanced Sampling
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <43CB942A.8070603 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1;
> format=flowed
> 
> msonoda at iqm.unicamp.br wrote:
> >> Ran Friedman wrote:
> >>> Hi,
> >>>
> 
=== message truncated ===


Dr. Absalom Zamorano Carrillo 
Profesor Titular A 
Programa Institucional de Biomedicina Molecular, ENMyH-IPN
Guillermo Massieu  Helguera  #239 Fracc. "La Escalera"
Ticomán, D.F. México, C.P  07320
Tel. (55) 57296000,  ext 55542




	
	
		
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