[gmx-users] Re: Re: temperature and pressure values

Marino Convertino marino.convertino at tiscali.it
Wed Jan 25 11:33:03 CET 2006

Dear Mark and gmxers,
thanks a lot for your reply.
I am checking md.log file after 5-days-computing-time of the same simulations.

About temperature and pressure I find these values:
Temperature    Pressure (bar)
 3.54285e+02    6.54609e+01

Temperature    Pressure (bar)
 3.52770e+02   -3.39396e+01

Temperature    Pressure (bar)
 3.54570e+02   -4.24080e+01

Temperature    Pressure (bar)
 3.54669e+02    4.29965e+01

Temperature    Pressure (bar)
3.51791e+02   -1.49698e+01

And so on...
Are these variations ok?
I wonder if temperature value ( constantly 2-4K over the fixed value) can be considered good.
And what about pressure variation?
I use these options in my NPT simulations:

Tcoupl              =  Berendsen
tc-grps              =  Protein  SOL
tau_t                =  0.1      0.1    ;time in ps
ref_t                =  350      350

Pcoupl                =  Berendsen
Pcoupltype          =  isotropic
tau_p                  =  1.0 
compressibility    =  4.5e-5
ref_p                   =  1.0

Should I modify any option in order to obtain a better convergence?
Should I use a different electrostatic treatment (PME)?
Sorry for the long message.

Thanks in advance
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