[gmx-users] berendsen P coupling and fluctuation properties
Mark.Abraham at anu.edu.au
Tue Aug 16 01:34:36 CEST 2011
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?
> I am interested in potential energy terms (g_energy bonded/non boned
I routinely struggle to see why people think they can learn anything
> and structural properties like rdf for a number of polymer molecules,
> system size around 3000 atoms.
> Thank you for your comments.
> 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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