[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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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