[gmx-users] why temperature result of DMSO simulation is so low
wangkelvin64 at gmail.com
Wed Jul 9 03:50:25 CEST 2008
thanks Justin for your help
i have used g_energy just now ,and it shows:
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?
> 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
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