[gmx-users] grompp warnings

[Travis Craddock]

I am trying to perform an energy minimization.  My em.mdp file is as follows:

title               = Tubulin 
cpp                 = /usr/bin/cpp ; location of cpp on mac 
define              = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] 
constraints         = none 
integrator          = steep 
dt                  = 0.002    ; ps ! 
nsteps              = 500 
nstlist             = 10  
ns_type             = grid 
rlist               = 0.9 
coulombtype         = PME ; Use particle-mesh ewald  
rcoulomb            = 0.9 
rvdw                = 1.0 
fourierspacing      = 0.12 
fourier_nx          = 0 
fourier_ny          = 0 
fourier_nz          = 0 
pme_order           = 4 
ewald_rtol          = 1e-5
optimize_fft        = yes 
; 
;       Energy minimizing stuff 
; 
emtol               = 1000.0 
emstep              = 0.01 




and I receive the following warnings:





WARNING 1 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 \cf0 title' in parameter file

WARNING 2 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 cpp' in parameter file

WARNING 3 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 define' in parameter file

WARNING 4 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 constraints' in parameter file

WARNING 5 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 integrator' in parameter file

WARNING 6 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 dt' in parameter file

WARNING 7 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 nsteps' in parameter file

WARNING 8 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 nstlist' in parameter file

WARNING 9 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 ns_type' in parameter file

WARNING 10 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 rlist' in parameter file

WARNING 11 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 coulombtype' in parameter file

WARNING 12 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 rcoulomb' in parameter file

WARNING 13 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 rvdw' in parameter file

WARNING 14 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 fourierspacing' in parameter file

WARNING 15 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 fourier_nx' in parameter file

WARNING 16 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 fourier_ny' in parameter file

WARNING 17 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 fourier_nz' in parameter file

WARNING 18 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 pme_order' in parameter file

WARNING 19 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 ewald_rtol' in parameter file

WARNING 20 [file em.mdp, line unknown]:
  Unknown left-hand '\f0\fs24 emtol' in parameter file




The program then terminates.  Can anyone explain what the problem is.

Thanks.