On 12/06/2012 9:14 PM, rama david wrote:
On Tue, Jun 12, 2012 at 4:40 PM, rama david <[email protected] <mailto:[email protected]>> 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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