[gmx-users] Nucleic Acid in vacuo
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 13 17:11:19 CEST 2011
Matthias Ernst wrote:
> Thank you very much for your help, Justin.
> I tried it with those mdp options:
> title = INITIAL_EM0
> cpp = /lib/cpp
> constraints = all-bonds
> integrator = md
> rlist = 0.0
> rcoulomb = 0.0
> rvdw = 0.0
> pbc = no
> This resulted in
> Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 1.88961e+01 6.04179e+01 5.60480e-04 3.74069e+01 -2.06394e+02
> LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
> 6.94305e-03 -5.66241e+01 -1.46290e+02 2.88457e-01 -1.46002e+02
> Temperature Pressure (bar) Constr. rmsd
> 1.21730e+00 0.00000e+00 0.00000e+00
> So, now the 1-4-values are slightly better (37.11 <-> 37.04 LJ, -207.7
> <-> -206.3 Coulomb), while the SR-LJ and Coulomb energys are at two
> orders of magnitude too small (LJ: 0.7127 <-> 0.0069430, Coulomb:
> -4354.5 <-> -56.62).
> In fact, I considered looking through the code but wanted to avoid it
> because I fear that there are so much optimisations implemented in
> Gromacs that I probably will not understand whats going on and why.
> Maybe I will try it, but first I will play with the forcefield
> parameters to see what happens if I switch everything off except certain
> pairs, then I can compare them.
> Besides, I'm wondering, is there a way to disable all optimisations and
> just do a "plain" Lennard-Jones and Coulomb evaluation in vacuo without
> any box, solvent, boundary conditions and without cutoffs in Gromacs?
That's essentially what you're doing with the .mdp file above. No box (pbc =
no), no cutoffs (r* = 0) and no solvent. There are options to disable
optimizations and use generic kernels in Gromacs, but I can't recall all of them
at the moment. Various environment variables are listed in the manual for
disabling optimizations and in the configuration help description.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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