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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