AMBER format PARM file and coordinate file can be read by NAMD, which allows one to use AMBER force field to carry out all types of simulations that NAMD has supported. NAMD can read PARM files in either the format used in AMBER 6 or the new format defined in AMBER 7. The output of the simulation (restart file, DCD file, etc.) will still be in traditional format that has been used in NAMD.
1. Polarizable parameters in AMBER are not supported.
2. NAMD does not support the 10-12 potential terms in some old AMBER versions. When non-zero 10-12 parameter is encountered in PARM file, NAMD will terminate.
3. NAMD has several exclusion policy options, defined by exclude. The way AMBER dealing with exclusions corresponds to the ``scaled1-4'' in NAMD. So for simulations using AMBER force field, one would specify ``exclude scaled1-4'' in the configuration file, and set 1-4scaling to the inverse value of SCEE as would be used in AMBER.
4. NAMD does not read periodic box lengths in PARM or coordinate file. They must be explicitly specified in NAMD configuration file.
5. By default, NAMD applies switching functions to the non-bond interactions within the cutoff distance, which helps to improve energy conservation, while AMBER does not use switching functions so it simply truncates the interactions at cutoff. However, if ``authentic'' AMBER cutoff simulations are desired, the switching functions could be turned off by specifying ``switching off'' in NAMD configuration file.
6. NAMD and AMBER may have different default values for
some parameters (e.g., the tolerance of SHAKE). One should check
other sections of this manual for accurate descriptions
of the NAMD options.
Following are two examples of the NAMD configuration file to read
AMBER force field and carry out simulation. They may help users
to select proper NAMD options for AMBER force field. For the
convenience of AMBER users, the AMBER 6 sander input files are
given in the left for comparison, which would accomplish similar
tasks in AMBER.
Example 1: Non-periodic boundary system, cutoff simulation
---AMBER---- ---NAMD--- TITLE &cntrl ntb=0, igb=2, # non-periodic, use cutoff for non-bond nstlim=1000, numsteps 1000 # Num of total steps ntpr=50, outputEnergies 50 # Energy output frequency ntwr=50, restartfreq 50 # Restart file frequency ntwx=100, DCDfreq 100 # Trajectory file frequency dt=0.001, timestep 1 # in unit of fs (This is default) tempi=0., temperature 0 # Initial temp for velocity assignment cut=10., cutoff 10 switching off # Turn off the switching functions scee=1.2, exclude scaled1-4 1-4scaling 0.833333 # =1/1.2, default is 1.0 scnb=2.0 scnb 2 # This is default &end amber on # Specify this is AMBER force field parmfile prmtop # Input PARM file ambercoor inpcrd # Input coordinate file outputname md # Prefix of output files
Example 2: Periodic boundary system, PME, NVE ensemble, using SHAKE algorithm
---AMBER---- ---NAMD--- TITLE &cntrl ntc=2, ntf=2, # SHAKE to the bond between each hydrogen and it mother atom rigidBonds all tol=0.0005, rigidTolerance 0.0005 # Default is 0.00001 nstlim=500, numsteps 500 # Num of total steps ntpr=50, outputEnergies 50 # Energy output frequency ntwr=100, restartfreq 100 # Restart file frequency ntwx=100, DCDfreq 100 # Trajectory file frequency dt=0.001, timestep 1 # in unit of fs (This is default) tempi=300., temperature 300 # Initial temp for velocity assignment cut=9., cutoff 9 switching off # Turn off the switching functions &end &ewald PME on # Use PME for electrostatic calculation # Orthogonal periodic box size a=62.23, cellBasisVector1 62.23 0 0 b=62.23, cellBasisVector2 0 62.23 0 c=62.23, cellBasisVector3 0 0 62.23 nfft1=64, PMEGridSizeX 64 nfft2=64, PMEGridSizeY 64 nfft3=64, PMEGridSizeZ 64 ischrgd=1, # NAMD doesn't force neutralization of charge &end amber on # Specify this is AMBER force field parmfile FILENAME # Input PARM file ambercoor FILENAME # Input coordinate file outputname PREFIX # Prefix of output files exclude scaled1-4 1-4scaling 0.833333 # =1/1.2, default is 1.0