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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20130805/2187c033/attachment.htm>


More information about the CP2K-user mailing list