Comparing the energy from cp2k and gromacs
Fahimeh Baftizadeh
fahimeh.b... at googlemail.com
Mon Aug 5 20:53:08 UTC 2013
Hello,
I have a system which contains only one molecule in gas phase. I wanna
compute its energy with cp2k and gromacs (for a test).
I am reading a pdb file and the force filed is in amber format, this is
cp2k input file:
&FORCE_EVAL
METHOD FIST
&MM
&FORCEFIELD
&SPLINE
EMAX_ACCURACY 500.0
EMAX_SPLINE 1000.0
EPS_SPLINE [hartree] 1.00000000E-07
&END
parm_file_name
/home/fbafti/work/nucleation/test-ff/single-mol/amber-1res.top
parmtype AMBER
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE pme
RCUT [angstrom] 8.0
EPSILON 1E-6
&END EWALD
&END POISSON
&PRINT
&FF_INFO
&END
&END
&END MM
&SUBSYS
&CELL
ABC 125.990 122.910 129.640
&END
&TOPOLOGY
COORD_FILE_NAME
/home/fbafti/work/nucleation/test-ff/single-mol/non-per.pdb
COORDINATE PDB
CONN_FILE_NAME
/home/fbafti/work/nucleation/test-ff/single-mol/amber-1res.top
CONN_FILE_FORMAT AMBER
&END TOPOLOGY
&END SUBSYS
STRESS_TENSOR ANALYTICAL
&END FORCE_EVAL
&GLOBAL
PROJECT paracetamol_single_mol
RUN_TYPE ENERGY
&END GLOBAL
I put a very large box size, just to be sure that there are no periodic
images in the energy estimation. The energy output of CP2K has a value
which is larger than zero and it is strange.
I performed a single step steepest decent with gromacs and I got another
value which is minus and makes more sense.
I already checked the electrostatic parameters and vdw ... I think they are
all similar while the energy difference coming from gromacs and
cp2k differs by almost 500 kj/mol and in gromacs is minus and in cp2k is a
plus value.
This is the gromacs input file:
integrator = steep
comm_mode = Linear
dt = 0.001
nsteps = 1
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 1
nstvout = 1
; Output frequency for energies to log file and energy file =
nstlog = 1
nstenergy = 1
nstxtcout = 1
xtc-precision = 1000000
xtc_grps = System
energygrps = System
pbc = xyz
nstlist = 10
epsilon_r = 1.
ns_type = grid ; or grid I don't know
coulombtype = pme
vdwtype = Cut-off
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = yes
rlist = 0.8
rcoulomb = 0.8
rvdw = 0.8
emtol = 1.0
Can anybody help me with that?
Thanks
Fahimeh
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