[gmx-users] Re: Press Equilibration

[Mark Abraham]

On 12/06/2012 9:14 PM, rama david wrote:
>
>
> On Tue, Jun 12, 2012 at 4:40 PM, rama david <ramadavidgroup at gmail.com 
> <mailto:ramadavidgroup at 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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