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psf2top Tests
resal81 edited this page Sep 23, 2013
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Notes:
- For these tests, first the
psffile was created and then converted to GROMACS format. - The
psffiles for these systems are intest/systems. - For more info on automation of these tests, see
test/systems/README.md. -
GMX-NAMDis the absolute difference (i.e.gromacs-namd) and% |diff|is(gromacs-namd)/namd * 100. - NAMD version is 2.9 and GROMACS version is 4.6.3.
- For testing your own systems, make sure they are minimized before comparing the energies.
Table 1. Summary of the rmsd of potential terms between GROMACS 4.6.3 and NAMD 2.9 (kcal/mol). Single and double correspond to the single and double-precision versions of GROMCAS.
-------------------------- ----------------- -----------------
natoms ff GMX-NAMD (double) GMX-NAMD (single)
-------------------------- ----------------- -----------------
AD peptide 22 CH27 0.000 0.000
POPC memb 9916 CH36 0.002 0.021
DOPC memb 10488 CH36 0.005 0.014
Lysozyme 1966 CH27 0.009 0.010
Cholesterol 74 CH36 0.000 0.000
Pr+Chol+Lip 27562 CH36 0.046 3.988
-------------------------- ----------------- -----------------
Table 2. Detail of the NAMD and GROMACS energies (kcal/mol) for select systems.
-----------------------------------------------------------
002 - AD in vacuum
NAMD GMX (double) GMX-NAMD % |diff| GMX (single) GMX-NAMD % |diff|
bond 79.78 79.78 -0.0001 0.000 79.78 -0.0001 0.000
angle 39.94 39.94 -0.0001 0.000 39.94 0.0001 0.000
dihedral 4.34 4.34 -0.0000 0.000 4.34 -0.0000 0.000
improper 0.06 0.06 -0.0000 0.069 0.06 -0.0000 0.069
coul -0.61 -0.61 0.0000 0.001 -0.61 0.0000 0.001
vdw 21.39 21.39 -0.0000 0.000 21.39 -0.0000 0.000
-----------------------------------------------------------
101 - POPC membrane in vaccum (CHARMM 36, 74 POPC, 9916 atoms)
NAMD GMX (double) GMX-NAMD % |diff| GMX (single) GMX-NAMD % |diff|
bond 134.20 134.20 -0.0004 0.000 134.20 -0.0013 0.001
angle 1611.89 1611.89 0.0000 0.000 1611.88 -0.0071 0.000
dihedral 3737.28 3737.28 0.0045 0.000 3737.28 0.0045 0.000
improper 10.31 10.31 -0.0000 0.000 10.31 -0.0000 0.000
coul -2377.17 -2377.17 -0.0014 0.000 -2377.13 0.0464 0.002
vdw -2663.91 -2663.91 -0.0036 0.000 -2663.89 0.0203 0.001
-----------------------------------------------------------
102 - DOPC membrane in vaccum (CHARMM 36, 76 DOPC, 10488 atoms)
NAMD GMX (double) GMX-NAMD % |diff| GMX (single) GMX-NAMD % |diff|
bond 143.88 143.88 -0.0003 0.000 143.88 -0.0007 0.001
angle 1591.22 1591.22 0.0016 0.000 1591.21 -0.0127 0.001
dihedral 4376.74 4376.74 0.0072 0.000 4376.72 -0.0167 0.000
improper 11.69 11.69 -0.0000 0.000 11.69 -0.0000 0.000
coul -2254.60 -2254.59 0.0092 0.000 -2254.59 0.0092 0.000
vdw -2896.05 -2896.05 0.0032 0.000 -2896.03 0.0271 0.001
-----------------------------------------------------------
201 - 1LYZ in vacuum (CHARMM 27+CMAP, 129 residues, 1966 atoms)
NAMD GMX (double) GMX-NAMD % |diff| GMX (single) GMX-NAMD % |diff|
bond 120.03 120.03 -0.0001 0.000 120.03 -0.0003 0.000
angle 354.94 354.94 0.0008 0.000 354.94 0.0008 0.000
dihedral 338.70 338.68 -0.0187 0.006 338.68 -0.0187 0.006
improper 19.78 19.78 0.0000 0.000 19.78 0.0001 0.000
coul -3995.40 -3995.41 -0.0134 0.000 -3995.41 -0.0134 0.000
vdw -568.16 -568.16 0.0009 0.000 -568.15 0.0033 0.001
-----------------------------------------------------------
301 - Cholesterol in vacuum (CHARMM 36, 74 atoms)
NAMD GMX (double) GMX-NAMD % |diff| GMX (single) GMX-NAMD % |diff|
bond 7.93 7.93 -0.0000 0.000 7.93 -0.0000 0.000
angle 58.62 58.62 0.0000 0.000 58.62 0.0000 0.000
dihedral 22.93 22.93 0.0000 0.000 22.93 0.0000 0.000
improper 0.00 0.00 0.0000 NA 0.00 0.0000 NA
coul -57.90 -57.90 -0.0001 0.000 -57.90 -0.0001 0.000
vdw 4.99 4.99 -0.0000 0.000 4.99 -0.0000 0.000
-----------------------------------------------------------
602 - Protein + chol + lipid
NAMD GMX (double) GMX-NAMD % |diff| GMX (single) GMX-NAMD % |diff|
bond 188594.57 188594.65 0.0721 0.000 188588.91 -5.6641 0.003
angle 108498.82 108498.80 -0.0138 0.000 108496.41 -2.4039 0.002
dihedral 14964.16 14964.09 -0.0706 0.000 14963.83 -0.3335 0.002
improper 746.82 746.82 0.0000 0.000 746.82 0.0000 0.000
coul -8781.08 -8781.09 -0.0118 0.000 -8781.17 -0.0835 0.001
vdw 196098.35 196098.30 -0.0451 0.000 196105.93 7.5791 0.004
-----------------------------------------------------------
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