On 12/06/2012 9:14 PM, rama david wrote:
On Tue, Jun 12, 2012 at 4:40 PM, rama david <ramadavidgr...@gmail.com
<mailto:ramadavidgr...@gmail.com>> 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 ?????
I am worried because of avg is -ve ...
The sign reflects the tendency of the system to expand or contract. No
big deal. Also, as Justin said, this value is not significantly
different from your reference value. See
http://www.gromacs.org/Documentation/Terminology/Pressure
Mark
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