psf2top Tests

I used psf2top.py to convert several psf files to GROMACS format and then compared the resulting single-point energies using NAMD 2.9 and GROMACS 4.6.3 (double-precision).

Results of select systems

Notes:

• For these tests, first the psf file was created and then converted to GROMACS format.
• The psf files for these systems are in test/systems.
• For more info on automation of these tests, see test/systems/README.md.
• GMX-NAMD is the absolute difference (i.e. gromacs-namd) and % |diff| is (gromacs-namd)/namd * 100.

Table 1. Summary of the difference between GROMACS and NAMD energies (kcal/mol). Percentages are shown in the parantheses.

    --------------------------  ------------
                  natoms  ff     potential
    --------------------------  ------------
      AD peptide      22  CH27  -0.00 ( 0.0)
       POPC memb    9916  CH36  -0.00 ( 0.0)
       DOPC memb   10488  CH36   0.02 ( 0.0)
        Lysozyme    1966  CH27  -0.03 ( 0.0)
     Cholesterol      74  CH36  -0.00 ( 0.0)
      Prot+Lipid   27562  CH36  -0.07 ( 0.0)
    --------------------------  ------------

Table 2. Detail of the NAMD and GROMACS energies (kcal/mol) for select systems.

    -----------------------------------------------------------
    002 - AD in vacuum
                       NAMD      GROMACS    GMX-NAMD   % |diff|
          bond        79.78        79.78     -0.0001      0.000
         angle        39.94        39.94     -0.0001      0.000
      dihedral         4.34         4.34     -0.0000      0.000
      improper         0.06         0.06     -0.0000      0.069
          coul        -0.61        -0.61      0.0000      0.001
           vdw        21.39        21.39     -0.0000      0.000

    -----------------------------------------------------------
    101 - POPC membrane in vaccum (CHARMM 36, 74 POPC, 9916 atoms)
                       NAMD      GROMACS    GMX-NAMD   % |diff|
          bond       134.20       134.20     -0.0004      0.000
         angle      1611.89      1611.89      0.0000      0.000
      dihedral      3737.28      3737.28      0.0045      0.000
      improper        10.31        10.31     -0.0000      0.000
          coul     -2377.17     -2377.17     -0.0014      0.000
           vdw     -2663.91     -2663.91     -0.0036      0.000

    -----------------------------------------------------------
    102 - DOPC membrane in vaccum (CHARMM 36, 76 DOPC, 10488 atoms)
                       NAMD      GROMACS    GMX-NAMD   % |diff|
          bond       143.88       143.88     -0.0003      0.000
         angle      1591.22      1591.22      0.0016      0.000
      dihedral      4376.74      4376.74      0.0072      0.000
      improper        11.69        11.69     -0.0000      0.000
          coul     -2254.60     -2254.59      0.0092      0.000
           vdw     -2896.05     -2896.05      0.0032      0.000

    -----------------------------------------------------------
    201 - 1LYZ in vacuum (CHARMM 27+CMAP, 129 residues, 1966 atoms)
                       NAMD      GROMACS    GMX-NAMD   % |diff|
          bond       120.03       120.03     -0.0001      0.000
         angle       354.94       354.94      0.0008      0.000
      dihedral       338.70       338.68     -0.0187      0.006
      improper        19.78        19.78      0.0000      0.000
          coul     -3995.40     -3995.41     -0.0134      0.000
           vdw      -568.16      -568.16      0.0009      0.000

    -----------------------------------------------------------
    301 - Cholesterol in vacuum (CHARMM 36, 74 atoms)
                       NAMD      GROMACS    GMX-NAMD   % |diff|
          bond         7.93         7.93     -0.0000      0.000
         angle        58.62        58.62      0.0000      0.000
      dihedral        22.93        22.93      0.0000      0.000
      improper         0.00         0.00      0.0000      0.000
          coul       -57.90       -57.90     -0.0001      0.000
           vdw         4.99         4.99     -0.0000      0.000

    -----------------------------------------------------------
    602 - Protein + chol + lipid (27562 atoms)
                       NAMD      GROMACS    GMX-NAMD   % |diff|
          bond    188594.57    188594.65      0.0721      0.000
         angle    108498.82    108498.80     -0.0138      0.000
      dihedral     14964.16     14964.09     -0.0706      0.000
      improper       746.82       746.82      0.0000      0.000
          coul     -8781.08     -8781.09     -0.0118      0.000
           vdw    196098.35    196098.30     -0.0451      0.000

    -----------------------------------------------------------

Tests setup

GROMACS simulations were run using:

$ grompp -f mdpfile -c pdbfile -p top.top -o topol.tpr
$ mdrun -nt 1 -s topol.tpr -rerun pdbfile -g gromacs.log

NAMD simulations were run using:

$ namd2 +p1 conf

GROMACS MDP file

integrator    = md
nsteps        = 0
nstlog        = 1
nstlist       = 0
ns_type       = simple
rlist         = 0
coulombtype   = cut-off
rcoulomb      = 0
rvdw          = 0
pbc           = no

NAMD configuration file

structure          [psffile]
coordinates        [pdbfile]

paratypecharmm      on
parameters         [parameter files]
exclude             scaled1-4
1-4scaling          1.0

switching           off
cutoff              1000
pairlistdist        1000
timestep            1.0
outputenergies      1
outputtiming        1
binaryoutput        no

outputname          namd
dcdfreq             1
temperature         300
run                 0