[gmx-users] Problem with PME + test particle insertion

Berk Hess gmx3 at hotmail.com
Fri Oct 8 10:45:18 CEST 2010


Have you checked that your numbers are converged?
Such differences can easily occur when you don't sample enough.
You will have to try very many orientations before you hit the right one
which satisfies all hydrogen bonds.

I tested PME a long time ago. Then it worked correctly.
But it could be that in the meantime something broke because of
changes in the pme code .


> Date: Fri, 8 Oct 2010 03:35:30 -0400
> From: kdaly at princeton.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Problem with PME + test particle insertion
> Hello Gromacs users,
> Recently I ran some test particle insertion simulations of TIP4P/2005
> water to measure  the chemical potential at 470 K and 0.861 g/cc. I
> found that the chemical potential was  20%-25% higher than literature
> values. I believe there may be a problem related to using PME with
> test-particle insertion.
> To test the PME code, I ran a very short TPI run of a water
> configuration with one molecule deleted. I forced insertions into the
> hole by using "tpic" mode. I compared the potential energies of these
> insertions with those obtained by simply taking the difference in
> potential energy of two md runs, where one contains the missing
> molecule and one has a hole instead. I ran mdrun in with the "-debug
> 1" option and added a line of code to tpi.c to print out the insertion
> locations. I am running the "release-4-5-patches
> origin/release-4-5-patches branch" of Gromacs 4.5.1.
> The LJ and short-range coulomb energies agree well, but the long-range
> coulomb energy does not. Compare 0.0229272 kJ/mol in TPI mode with
> -8.771680 kJ/mol in MD mode. Note that the total energy changes are
> -61.19020 and -69.97481, respectively.
> Input files for these tests can be found at
> http://bugzilla.gromacs.org/show_bug.cgi?id=590 .
> -Kevin
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