[gmx-users] NPT: pressure coupling
David
spoel at xray.bmc.uu.se
Mon Mar 7 21:45:24 CET 2005
On Mon, 2005-03-07 at 12:36 -0800, Nancy Deng wrote:
> Thanks David for your response. But I'm still confusing. Are you suggesting
> me to increase the box size where more h2o will be included in order to get
> less pressure fluctuation.
No, I'm just saying it's fine.
>
> Or, is there any other option to specify the NPT ensemble simulation???
No. You can have different parameters. Longer coupling time is fine for
long simulations. Will have slightly large fluctuations, but same
average.
>
>
> Thanks,
>
> nancy
> ----- Original Message -----
> From: "David" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Monday, March 07, 2005 11:56 AM
> Subject: Re: [gmx-users] NPT: pressure coupling
>
>
> On Mon, 2005-03-07 at 09:54 -0800, Nancy Deng wrote:
> > Dear All,
> >
> > After my system equilibrated, I have performed 2ns production phase md
> > simulation. I am expecting my calulation is in the NPT ensemble. From
> > the g_energy analysis, temperature is well consistent around 300K, but
> > the pressure is fluctuating significantly from -340 bar 300 bar.
> this is perfectly normal. increasing the number of atoms by a factor of
> four will reduce the fluctuations by a factor of two.
>
> >
> > The parameter setup in the .mdp file is as following:
> >
> > *******
> > Pcoupl = berendsen
> > pcoupltype = isotropic
> > tau_p = 1
> > compressibility = 4.5e-5
> > ref_p = 1
> > ********
> >
> > Could anyone please let me kwow what's wrong in the file setup???
> >
> >
> > Thanks,
> >
> > nancy
> >
> >
> >
> > ----- Original Message -----
> > From: Marc Kreissler
> > To: Discussion list for GROMACS users
> > Sent: Friday, March 04, 2005 10:11 AM
> > Subject: Re: [gmx-users] DNA/RNA records for OPLS force
> > fieldin GROMACS format.
> >
> >
> > david.evans at ulsop.ac.uk a écrit:
> > > Hi,
> > >
> > > I think that 60 water molecules is far too few. One would
> typically
> > > add a few thousand in a box extending about 10 angstroms from
> > > the solute.
> > >
> > > If it's not too heretical for this list, might I suggest looking
> > > at the DNA tutorial on the Amber web site? This, and the
> > > cited references, give a good idea of what people do in the
> > > successful DNA simulations to date.
> > >
> > > good luck,
> > >
> > > Dave
> > > -
> > >
> > > > after some work and many "try and error" i have succeeded
> to
> > > > build the various files which are necessary for running
> Gromacs
> > > > calculations on a DNA_decamer with about 60 water
> molecules,
> > > > 2 Ca++ ions and 15 Na+ ions to neutralise the excess
> negative
> > > > charges due to phosphate groups.
> > > >
> > > > i get a surprising result after 1ns of simulation ( about
> 3hours
> > > >
> > > on a Linux_PC) :
> > >
> > > > the double-helix ends up in a dissociated state.
> > > >
> > > > for this calculation i use - a triclinic box
> > > > - pme for
> electrostatics
> > > > - T_coupling at 300K
> > > > - no P_coupling
> > > > - oplsaar force
> field
> > > >
> > > > my experience in MD_simulations is not tremendous,
> especially
> > > > concerning the simulation parameters.
> > > >
> > > > - i am wondering if i have choosen the right box form ?
> > > > - what about the box dimensions ?
> > > > - may be the number of water molecules is too small for this
> system
> > > >
> > > ?
> > >
> > > > - and last but not least i don't know if the periodic
> boundary
> > > >
> > > conditions
> > >
> > > > are on or off ?
> > > >
> > > > a lot of questions.
> > > >
> > > > i would appreciate your helpfull advices.
> > > >
> > > > merci , cordialement
> > > >
> > > > marc kreissler
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > >
> > > >
> > > >
> > > _______________________________________________
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> > >
> > >
> > bonsoir david evans,
> >
> > thank's for the usefull hint to have a look at the "DNA
> > tutorial"
> > located on the Amber website. "keep on learning,
> > learning,..." ( a quote from vladimir
> > illitch lenin).
> >
> > cordialement,
> > marc kreissler
> >
> >
> >
> >
> >
> > ______________________________________________________________
> >
> > _______________________________________________
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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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