<div>thanks Justin for your help</div>
<div> </div>
<div>i have used g_energy just now ,and it shows:</div>
<div> </div>
<div>temperature 290.358</div>
<div>T-DMSO 290.420</div>
<div>T-SOL 290.306</div>
<div> </div>
<div> <br><br> </div>
<div><span class="gmail_quote">2008/7/9, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">What does g_energy tell you (from the .edr file)? Note the output of<br>g_traj -h: "No corrections are made for constrained degrees of freedom!"<br>
If you're applying constraints, that may have some effect on the result.<br>Also, you should have been able to see the system temperature the whole<br>time during the simulation in the .log file - what does it say?<br>
<br>-Justin<br><br>wang kelvin wrote:<br>><br>> Hi<br>><br>> I am doing simulation of the mixture of DMSO and water . I put 512<br>> DMSO moleculers and 917 water moleculers in a box . The given<br>> temperature is 290K , and pressure is 1 bar .<br>
><br>> After simulation completed , I used g_traj to produce xvg file , then<br>> I saw that simulation gave a temperatue result of about 200K.<br>><br>> Some documents tell me DMSO simulation usually gives 5-7 K lower than<br>
> you have given in mdp file ,e.g. if you give 300K in mdp file , but<br>> simulation result gives 295 K .<br>><br>> I wonder why my simulation gave so low temperture ,any hints is<br>> appreciated.<br>><br>
> Part of my mdp file:<br>><br>> Tcoupl = berendsen<br>><br>> tau_t = 0.1 0.1<br>><br>> tc-grps = DMSO SOL<br>><br>> ref_t = 290 290<br>><br>> ; Pressure coupling is not on<br>><br>> Pcoupl = parrinello-rahman<br>
><br>> tau_p = 0.5<br>><br>> compressibility = 4.5e-5<br>><br>> ref_p = 1.0<br>><br>> ; Generate velocites is on at 190 K.<br>><br>> gen_vel = yes<br>><br>> gen_temp = 290.0<br>><br>
> gen_seed = 173529<br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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<br>--<br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br>_______________________________________________<br>
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</blockquote></div><br>