[gmx-users] NPT: pressure coupling

[Nancy Deng]

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.

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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  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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