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

[Sunita Patel]

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.

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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