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 <[EMAIL PROTECTED]>: > > 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 > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > 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 > > ======================================== > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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