[gmx-users] NPT: pressure coupling
parinald at unsl.edu.ar
parinald at unsl.edu.ar
Mon Mar 7 21:52:51 CET 2005
maybe you have to take a look the termodinamic phase diagram PV for water.
if you have very little V (and dV) then you have a "huge" dP.
Pablo.
> 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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>>
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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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