mcgrath wrote:
Hi. I'm fairly new to GROMACS, and I've been using it to run some
classical MD simulations. In order to be sure that I'm using the
correct force field (I had to add a molecule to CHARMM27), I'm comparing
it to another simulation code that I know well, CP2K (using GROMACS
4.5.4 and a recent CVS version of CP2K). Sadly, they are giving me
energy differences of about a factor of 2 for a 75000 atom protein+water
system. As far as I can tell, I'm using the same PME parameters, and
there's not a big change in energy when I change those, anyway. I've
been able to confirm that it's not a global problem (computing the
energy of only the 25,000 TIP3P waters give a result to within 1%, which
is not perfect, but better...I seem the same 1% difference if I only use
29 waters). For a smaller system (using the molecule I added), the
total energy is incorrect, but the torsion and improper torsions are
good to within 1%. So it looks like my topology is perhaps being
incorrectly specified, or the parameters for them.
Which energy terms show the discrepancy in the case of the twofold difference?
What I would like to do is get GROMACS to print out all the charges (the
electrostatics/nonbonded are also different) that it is actually using,
as well as the force field parameters being used. By using mdrun -v
-debug I get some of that, but lines like
You don't need mdrun -debug for this. The topology is static, so run gmxdump on
your .tpr file. This will map all parameters to each atom.
-Justin
c6= 1.48497790e-03, c12= 6.58807176e-06
c6= 3.78914556e-04, c12= 4.08982345e-07
c6= 2.02168059e-03, c12= 4.42785949e-06
c6= 1.71635114e-03, c12= 4.54480232e-06
c6= 2.60732602e-03, c12= 6.42257237e-06
c6= 3.75109637e-04, c12= 2.77185705e-07
c6= 1.98187144e-03, c12= 5.24788538e-06
c6= 6.18919948e-05, c12= 7.54611396e-09
c6= 1.73354731e-03, c12= 5.36550624e-06
c6= 4.41942073e-04, c12= 4.93156790e-07
c6= 6.79507386e-03, c12= 2.55060841e-05
c6= 1.61714898e-03, c12= 3.18964840e-06
c6= 2.48678902e-04, c12= 2.13336705e-07
are somewhat unclear. They are obviously non-bonded terms, but
corresponding to which atoms? The same goes for the bond angles and
torsions printed later. The worst-case scenario is that I have to poke
around in the source files, which I would to avoid so I'm hoping there
is some documentation or more switches I can flip somewhere. Thanks!
Cheers, Matt
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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