On 6/12/12 7:10 AM, rama david wrote:
Hi Gromacs Friends,
I did NPT for 100 ps with folowing parameter
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
I got foolowing result by using g_energy
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Pressure -3.99675 0.66 518.604 -2.89716 (bar)
Is it is right??
Is the system is equilibrated or I need to give more time ?????
Pressure is very hard to converge and often requires more than 100 ps. There
are numerous discussions on this topic, so please refer to the list archive for
many useful posts. Your pressure value is basically 4 ± 519. Is that
significantly different from 1? No, likely not, but you can achieve a value of
1 or very close if you equilibrate for a sufficiently long time.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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