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
--
========================================
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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