Hi Dallas Warren,<br><br>1. The molecules are the same. But we built the system in different method, and used different number of molecules. <br>2. We both used the oplsaa all-atom force field, but the parameters are a little different.
<br>3. I used gromacs. The reference used MDynaMix.<br>4. The unit of energy are both KJ/mol<br><br>I think no matter what softwares or systems, the energies should almost the same. At least, they should not deviate to much? is it right?
<br><br><br>PS: For the pressure, I used Berendsen pressure coupling.<br><br><div><span class="gmail_quote">2006/9/21, Dallas B. Warren <<a href="mailto:Dallas.Warren@vcp.monash.edu.au">Dallas.Warren@vcp.monash.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;">>1. I simualted a pure small molecule system. All the simulation is ok.<br>But
<br>>when I use g_energy to calculate the energy of bond, angle, lj, and<br>coloumb,<br>>it gives the following energy. The energies is much bigger, about<br>50-100 times<br>>bigger than the reported data. What's wrong?
<br><br>Well, that depends on what the reported data actually is to whether you<br>can actually make the comparison.<br><br>Is it for exactly the same system with the same forcefield?<br><br>Is it for the entire system or for per molecule?
<br><br>Catch ya,<br><br>Dr. Dallas Warren<br>Lecturer<br>Department of Pharmaceutical Biology and Pharmacology<br>Victorian College of Pharmacy, Monash University<br>381 Royal Parade, Parkville VIC 3010<br><a href="mailto:dallas.warren@vcp.monash.edu.au">
dallas.warren@vcp.monash.edu.au</a><br>+61 3 9903 9524<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble<br>a nail.<br>_______________________________________________
<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</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
<br>**********************************************