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Hi,<br><br>Have you checked that your numbers are converged?<br>Such differences can easily occur when you don't sample enough.<br>You will have to try very many orientations before you hit the right one<br>which satisfies all hydrogen bonds.<br><br>I tested PME a long time ago. Then it worked correctly.<br>But it could be that in the meantime something broke because of<br>changes in the pme code .<br><br>Berk<br><br>> Date: Fri, 8 Oct 2010 03:35:30 -0400<br>> From: kdaly@princeton.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Problem with PME + test particle insertion<br>> <br>> Hello Gromacs users,<br>> <br>> Recently I ran some test particle insertion simulations of TIP4P/2005<br>> water to measure the chemical potential at 470 K and 0.861 g/cc. I<br>> found that the chemical potential was 20%-25% higher than literature<br>> values. I believe there may be a problem related to using PME with<br>> test-particle insertion.<br>> <br>> To test the PME code, I ran a very short TPI run of a water<br>> configuration with one molecule deleted. I forced insertions into the<br>> hole by using "tpic" mode. I compared the potential energies of these<br>> insertions with those obtained by simply taking the difference in<br>> potential energy of two md runs, where one contains the missing<br>> molecule and one has a hole instead. I ran mdrun in with the "-debug<br>> 1" option and added a line of code to tpi.c to print out the insertion<br>> locations. I am running the "release-4-5-patches<br>> origin/release-4-5-patches branch" of Gromacs 4.5.1.<br>> <br>> The LJ and short-range coulomb energies agree well, but the long-range<br>> coulomb energy does not. Compare 0.0229272 kJ/mol in TPI mode with<br>> -8.771680 kJ/mol in MD mode. Note that the total energy changes are<br>> -61.19020 and -69.97481, respectively.<br>> <br>> Input files for these tests can be found at<br>> http://bugzilla.gromacs.org/show_bug.cgi?id=590 .<br>> <br>> -Kevin<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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