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

[Justin A. Lemkul]

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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