rama david wrote:
Hi Gromacs user ,
In justin tutorial protein-ligand complex..
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/08_MD.html
the production md.mdp has following parameter for Pressure and
Temperature coupling
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_JZ4 Water_and_ions ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for
each group, in K
; Pressure coupling is off
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of
water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
My query is ..Why Pressure Coupling is off in production MD run ???
Pressure coupling is on, hence:
pcoupl = Parrinello-Rahman
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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