[gmx-users] Re: gmx-users digest, Vol 1 #1400 - 4 msgs

[David]

On Sat, 2004-05-01 at 04:23, Sunita Patel wrote:
> Dear David,
> 
> Thanks.
> Actually I came across the article J. Mol. Biol., 2000, 296, 1257-82 where
> the pressure was maintained at ~26 atm for 498 K simlation. In that
> context I asked that question.
> 
Of course you can look up what pressure is needed at a given temperature
to keep real water liquid, but the simulated water may be different.
There is a Biophys. J. paper from the Van Gunsteren group adressing this
IIRC.


> Regards,
> Sunita
> -------------------------------------------------------------------------------
> Sunita Patel
> Biophysical Lab.,
> Dept. of Chemistry,
> Indian Institute of Technology(IIT) Bombay,
> Powai, Mumbai, Maharashtra,
> INDIA-400076.
> 
> Tel: (91)-22-25764176.
> Email:sunita at chem.iitb.ac.in
> -------------------------------------------------------------------------------
> 
> 
> 
> On Thu, 29 Apr 2004 gmx-users-request at gromacs.org wrote:
> 
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> > Today's Topics:
> >
> >    1. SA again (Nuno R. L. Ferreira)
> >    2. reference pressure,NPT, SPC water, 400 K (Sunita Patel)
> >    3. reference pressure,NPT, SPC water, 400 K (Sunita Patel)
> >    4. Re: reference pressure,NPT, SPC water, 400 K (David)
> >
> > --__--__--
> >
> > Message: 1
> > From: "Nuno R. L. Ferreira" <nunolf at ci.uc.pt>
> > Organization: Universidade Coimbra
> > To: gmx-users at gromacs.org
> > Date: Wed, 28 Apr 2004 19:49:16 +0100
> > Subject: [gmx-users] SA again
> > Reply-To: gmx-users at gromacs.org
> >
> > Hi Osmany
> >
> > Reading your question again, the interpretation was a bit different.
> > You were talking about constraints (LINCS,SHAKE,SETTLE) and I was thinking
> > about position restraints.
> >
> > IMHO, I think you should use constraints during your SA run.  If you do not
> > use bond contraints for e.g., you have to be carefull with your time step.
> > So if you are going to use dt=0.002 use constraints, if not, the bond lenghts
> > will be outside "normal" ranges, and in place of getting good structures, you
> > will have bad ones.
> >
> > Regards,
> > Nuno
> >
> > P.S. About not using water, I do not know. Any insights here?
> >
> > --__--__--
> >
> > Message: 2
> > Date: Thu, 29 Apr 2004 13:16:47 -0500 (CDT)
> > From: Sunita Patel <sunita at chem.iitb.ac.in>
> > To: Gromacs <gmx-users at gromacs.org>
> > Subject: [gmx-users] reference pressure,NPT, SPC water, 400 K
> > Reply-To: gmx-users at gromacs.org
> >
> > Dear gmx-users,
> >
> > I want to do a NPT simulation at temperature 400 K for protein in box of
> > SPC water. How much I should keep the reference pressure to keep the liquid state of SPC
> > water.
> >
> > Thanks for any suggesstion.
> >
> > Regards,
> > Sunita
> >
> > -------------------------------------------------------------------------------
> > Sunita Patel
> > Biophysical Lab.,
> > Dept. of Chemistry,
> > Indian Institute of Technology(IIT) Bombay,
> > Powai, Mumbai, Maharashtra,
> > INDIA-400076.
> >
> > Tel: (91)-22-25764176.
> > Email:sunita at chem.iitb.ac.in
> > -------------------------------------------------------------------------------
> >
> >
> >
> >
> > --__--__--
> >
> > Message: 3
> > Date: Thu, 29 Apr 2004 13:23:23 -0500 (CDT)
> > From: Sunita Patel <sunita at chem.iitb.ac.in>
> > To: Gromacs <gmx-users at gromacs.org>
> > Subject: [gmx-users] reference pressure,NPT, SPC water, 400 K
> > Reply-To: gmx-users at gromacs.org
> >
> >
> > Dear gmx-users,
> >
> > I want to do a NPT simulation at temperature 400 K for protein in box of
> > SPC water by using GROMOS forcefield. How much I should keep the reference
> > pressure to keep the liquid state of SPC water.
> >
> > Thanks for any suggesstion.
> >
> > Regards,
> > Sunita
> >
> > -------------------------------------------------------------------------------
> > Sunita Patel
> > Biophysical Lab.,
> > Dept. of Chemistry,
> > Indian Institute of Technology(IIT) Bombay,
> > Powai, Mumbai, Maharashtra,
> > INDIA-400076.
> >
> > Tel: (91)-22-25764176.
> > Email:sunita at chem.iitb.ac.in
> > -------------------------------------------------------------------------------
> >
> >
> >
> >
> > --__--__--
> >
> > Message: 4
> > Subject: Re: [gmx-users] reference pressure,NPT, SPC water, 400 K
> > From: David <spoel at xray.bmc.uu.se>
> > To: gmx-users at gromacs.org
> > Date: Thu, 29 Apr 2004 11:04:57 +0200
> > Reply-To: gmx-users at gromacs.org
> >
> > On Thu, 2004-04-29 at 20:16, Sunita Patel wrote:
> > > Dear gmx-users,
> > >
> > > I want to do a NPT simulation at temperature 400 K for protein in box of
> > > SPC water. How much I should keep the reference pressure to keep the liquid state of SPC
> > > water.
> >
> > it won't evaporate at 400 K. It's not water, only SPC.
> >
> > > Thanks for any suggesstion.
> > >
> > > Regards,
> > > Sunita
> > >
> > > -------------------------------------------------------------------------------
> > > Sunita Patel
> > > Biophysical Lab.,
> > > Dept. of Chemistry,
> > > Indian Institute of Technology(IIT) Bombay,
> > > Powai, Mumbai, Maharashtra,
> > > INDIA-400076.
> > >
> > > Tel: (91)-22-25764176.
> > > Email:sunita at chem.iitb.ac.in
> > > -------------------------------------------------------------------------------
> > >
> > >
> > >
> > > _______________________________________________
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> > --
> > 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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> > End of gmx-users Digest
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> 
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-- 
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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