Hi Mark,<br><br><div><span class="gmail_quote">2006/9/22, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Qiao Baofu wrote:<br><br>What is this "reported data"?</blockquote><div><br><br>The reported data are (KJ/mol) : Bond 27; Angle: 30; LJ: -27; electrostatic -530.<br><br>Some days ago, I run again in gromacs but using all the "reported" force-field parameters. In the end, I get the similar result as listed in the first letter.
<br><br>Have someone compared the energy of gromacs with other software? <br><br></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">> Statistics over 5000001 steps [
0.0000 thru 5000.0000 ps ], 6 data sets<br>><br>> Energy Average RMSD Fluct. Drift<br>> Tot-Drift<br>> -------------------------------------------------------------------------------
<br>><br>> Bond 2869.13 93.6564 93.6562 0.000137548<br>> 0.687742<br>> Angle 7303.46 140.13 140.13 0.000189867<br>> 0.949334<br>> Ryckaert-Bell.
3326.2 97.6245 97.6161 -0.000890977 -4.45489<br>> LJ-(SR) -7616.62 138.684 138.67 -0.00138166<br>> -6.90831<br>> Coulomb-(SR) -22763.2 138.465 138.238 -0.00549019 -
27.451<br>> Potential -64743 219.54 219.203 -0.00842365<br>> -42.1182<br>><br>> 2. I used the "isotropic!!" pressure coupling, but at the end of the<br>> .log file (in the average section), it says:
<br>><br>> Pressure (bar)<br>> -2.64364e+01 3.71622e+01 3.00738e+00<br>> 3.71622e+01 1.32932e+01 -2.49814e+01<br>> 3.00738e+00 -2.49814e+01 1.61609e+01<br>><br>> The Pxx, Pyy, Pzz are not equal. Why?
<br><br>What is the geometry of your system?</blockquote><div><br>It is imidazolium-based material.<br><br><br>PS: The following processes are used: <br> 1. md1: NTV (nose-hoover for T coupling) 300ps<br> 2. md2: NTP (Berendsen for T & P coupling) T=425K, P=1bar, 500ps, tau_p=1
<br> 3. in md3.mdp: gen_temp = no unconstrained-start = yes<br> grompp -e md2.edr -f md3.mdp -c md2.gro -p -o <br> md3: NTP (nose-hoover for T coupling & Parrillo-rahman for P coupling) T=425K, P=1bar, 3000ps, tau_p=4
<br> 4. collect data.<br><br>g_energy<br> Energy Average RMSD Fluct. Drift Tot-Drift<br> -------------------------------------------------------------------------------<br> Pressure-(bar)
1.75443 931.231 931.227 -0.00331938 -9.95814<br><br>In md3.log<br> Pressure (bar)<br> 3.37452e+01 -1.01961e+02 1.77413e+01<br> -1.01961e+02 -7.66155e+00 -4.13047e+01<br> 1.77413e+01 -4.13047e+01
-2.08203e+01<br><br>Even though I used the Berendsen P coupling to relax the pressure firstly, and then use the Parrilo-rahman, the final result of pressure deviates much from what I want! After md2 and md3, I both used g_velacc to check the velocity-corelation function.
<br><br><br>Who has such experience? How to solve it?<br><br> </div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Mark<br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies<br>Max-von-Laue-Str. 1<br>60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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