[gmx-users] berendsen P coupling and fluctuation properties

[Elisabeth]

Hello,

Thank you. I am looking at potential energies to calculate vaporization
heat. I wanted to know how the fact that berendsen does not lead to correct
ensemble is affecting total potential energy of the system. I have an
unclear image of "correct ensemble". Does this mean whatever output I am
getting from my runs are unreliable?

Appreciate any clarification.

Thank you,
Best,

On 15 August 2011 19:34, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

>  On 16/08/2011 7:05 AM, Elisabeth wrote:
>
> Dear all,
>
> I noticed that applying Parrinello-Rahman (PR) pressure coupling even after
> equilibration with berendsen does not lead to target value for pressure when
>
>
> ;        Bonds
> constraints             = none
>
> is used.
>
>
> The use of constraints and the integration step size is linked. Roughly
> speaking, no constraints should accompany a 0.5 fs time step, H-bond
> constraints with 1fs and all constraints with 2fs. Haphazard changes to .mdp
> files have all kinds of these "gotchas".
>
>
>  I tried Berendsen for to get fixed pressure ( 50 bar) but in the next run
> PR even for long time is giving 52 bar. This is the case for other target
> pressures too.
>
>
> You need to be sure to collect statistics only after equilibration, and
> consider whether the observed variation is consistent with convergence to a
> given value.
>
>
>
> So this made me select Berenden which is giving target pressure values but
> my concern is whether my results are reliable because BR does not give the
> exact ensemble as PR. I read somewhere on the list that fluctuation
> properties can not be calculated when BR is used.  What does "fluctuation
> property" mean?
>
>
> BR does not produce the correct ensemble. I forget the details about why,
> but there are references in the T-coupling section of the manual you should
> consider.
>
>
> Does this mean that any property calculated form fluctuations of some other
> quantity can not be obtained>? like heat capacity which is defined based on
> enthalpy fluctuations?
>
>
> IIRC, yes.
>
>
> I am interested in potential energy terms (g_energy bonded/non boned terms)
>
>
>
> I routinely struggle to see why people think they can learn anything from
> these.
>
>
> and structural properties like rdf for a number of polymer molecules,
> system size around 3000 atoms.
>
> Thank you for your comments.
> Best,
>
> constraints             = none
>
> ;        Run control
> integrator          =  md
> dt                  =  0.001
> nsteps              =  5000000
> nstcomm             =  100
>
>
> nstenergy           =  100
> nstxout             =  100
> nstlist             =  10
> ns_type             =  grid
>
> coulombtype         =  Shift
> vdw-type            =  Shift
> rcoulomb-switch     =  0
> rvdw-switch         =  0.9 ;0
>
> ;        Cut-offs
> rlist               =  1.25
> rcoulomb            =  1.0
> rvdw                =  1.0
>
> Tcoupl              =  v-rescale
> tc-grps             =  System
> tau_t               =  0.1
> ref_t               =  300
>
> Pcoupl              =  berendsen
> Pcoupltype          =  isotropic
> tau_p               =  1
> compressibility     =  3.5e-5
> ref_p               =  10
>
>
> gen_vel             =  no
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
>
>
>
>
>
>
>
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