[gmx-users] NPT: pressure coupling

[David]

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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