Comparing the energy from cp2k and gromacs

Fahimeh Baftizadeh fahimeh.b... at googlemail.com
Tue Aug 6 18:00:11 CEST 2013


Hello everyone, 

I thought maybe it will be helpful if I just put here my input files and 
someone else run it if it is possible for you. In fact it seems very 
trivial but I checked the parameters and I don't understand why the Energy 
is positive! 

I am doing just a single step energy calculation of a molecule. 
Thanks for your help

Fahimeh



On Monday, August 5, 2013 4:53:08 PM UTC-4, Fahimeh Baftizadeh wrote:
>
> 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/20130806/b0d693ce/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Paracetamol_opt_cell_md.inp
Type: chemical/x-gamess-input
Size: 897 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20130806/b0d693ce/attachment.inp>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: amber-1res.top
Type: application/octet-stream
Size: 17698 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20130806/b0d693ce/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: non-per.pdb
Type: chemical/x-pdb
Size: 1655 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20130806/b0d693ce/attachment.pdb>


More information about the CP2K-user mailing list