[gmx-users] Discrepancy in a single point energy simulation between Gromacs and Namd.

IÑIGO SAENZ inigo.saenz01 at estudiant.upf.edu
Fri Nov 7 17:45:54 CET 2014

Hi all,

I've got a system of a protein inside a cube of water parametrized with the
amber ff99SB force-field. I have converted the .prmtop and .pdb files of
this system into a .gro and .top by means of ACPYPE. The problem is that
when I perform the single point energy calculation of these system with
Namd and Gromacs I obtain very opposing results in the Electrostatic energy
results and I suspect that I'm overlooking some details in the .mdp file
or  in the namd input file. I paste you the results that I obtain with NAMD
and gromacs and also the configuration files.

BOND:     38088.4829     38081.7399
ANGLE:    1573.6867      1573.7189
DIHEDRAL: 9873.2782      9872.7127
COULOMB:  -179655.6187   141241 (1-4 interactions)  -1.84836e+07 (short
VDW:      21796.8418     21797.2514

First column corresponds to NAMD results and the second one to Gromacs
Now, the *SPE.mdp file*

define                   = -DFLEXIBLE
integrator               = md
nsteps                   = 0
dt                       = 0.001
constraints              = none
nstcomm                  = 1
ns_type                  = simple
nstlist                  = 1
coulombtype              = cut-off
vdw_modifier             = none
coulomb_modifier         = none
rlist                    = 0.9
rcoulomb                 = 0.9
rvdw                     = 0.9
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 1
pbc                      = xyz
nstlog                   = 1
nstenergy                = 1
nstvout                  = 1
nstfout                  = 1
nstxtcout                = 1
comm_mode                = ANGULAR
continuation             = yes

*NAMD.conf file:*

rigidBonds     none
timestep       2
temperature    0
cutoff         9
switching      off
PME            off
cellBasisVector1   117.210 0  0
cellBasisVector2   0  94.119  0
cellBasisVector3   0  0  78.923
# NAMD doesn't force neutralisation of charge
amber          on  # Specify this is AMBER force field
parmfile       parameters  # Input PARM file
ambercoor      s.inpcrd  # Input coordinate file
outputname     run_namd  # Prefix of output files
exclude        scaled1-4
1-4scaling     0.8333  # =1/1.2, default is 1.0
run            0 ;# 2ps

I should mention that in .gro I put the box size correctly, the same values
that the box-size values that appear in the NAMD.conf file divided by 10 to
convert them to nanometers.

I'm desperate with this error, please, any help would be highly
appreciated! If you need more information about this problem, feel free to
ask me.

Thank you very much in advance!

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