[gmx-users] NPT: pressure coupling

Nancy Deng jdeng at adrik.bchs.uh.edu
Mon Mar 7 21:36:46 CET 2005


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.

Or, is there any other option to specify the NPT ensemble simulation???


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
>         > >
>         > >
>         > >
>         > >
>         > >
>         > >
>         > >
>         > > _______________________________________________
>         > > gmx-users mailing list
>         > > gmx-users at gromacs.org
>         > > http://www.gromacs.org/mailman/listinfo/gmx-users
>         > > Please don't post (un)subscribe requests to the list. Use the
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>         > >
>         > >
>         > >
>         > >
>         > _______________________________________________
>         > gmx-users mailing list
>         > gmx-users at gromacs.org
>         > http://www.gromacs.org/mailman/listinfo/gmx-users
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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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