[gmx-users] berendsen P coupling and fluctuation properties

[Mark Abraham]

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                  =  0.002
> 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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