[gmx-users] berendsen P coupling and fluctuation properties

Elisabeth katesedate at gmail.com
Mon Aug 15 23:05:15 CEST 2011

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. 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.

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?

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 terms)
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110815/47e0664d/attachment.html>

More information about the gromacs.org_gmx-users mailing list