[gmx-users] why temperature result of DMSO simulation is so low

[wang kelvin]

thanks Justin for your help

i have used g_energy just now ,and it shows:

temperature 290.358
T-DMSO     290.420
T-SOL        290.306




2008/7/9, Justin A. Lemkul <jalemkul at vt.edu>:
>
> What does g_energy tell you (from the .edr file)? Note the output of
> g_traj -h: "No corrections are made for constrained degrees of freedom!"
> If you're applying constraints, that may have some effect on the result.
> Also, you should have been able to see the system temperature the whole
> time during the simulation in the .log file - what does it say?
>
> -Justin
>
> wang kelvin wrote:
> >
> > Hi
> >
> > I am doing simulation of the mixture of DMSO and water . I put 512
> > DMSO moleculers and 917 water moleculers in a box . The given
> > temperature is 290K , and pressure is 1 bar .
> >
> > After simulation completed , I used g_traj to produce xvg file , then
> > I saw that simulation gave a temperatue result of about 200K.
> >
> > Some documents tell me DMSO simulation usually gives 5-7 K lower than
> > you have given in mdp file ,e.g. if you give 300K in mdp file , but
> > simulation result gives 295 K .
> >
> > I wonder why my simulation gave so low temperture ,any hints is
> > appreciated.
> >
> > Part of my mdp file:
> >
> > Tcoupl = berendsen
> >
> > tau_t = 0.1 0.1
> >
> > tc-grps = DMSO SOL
> >
> > ref_t = 290 290
> >
> > ; Pressure coupling is not on
> >
> > Pcoupl = parrinello-rahman
> >
> > tau_p = 0.5
> >
> > compressibility = 4.5e-5
> >
> > ref_p = 1.0
> >
> > ; Generate velocites is on at 190 K.
> >
> > gen_vel = yes
> >
> > gen_temp = 290.0
> >
> > gen_seed = 173529
> >
> > ------------------------------------------------------------------------
> >
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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