Hi there, I have a very simple case of a tri alanine (AAA). You can use tleap to create such peptide and save the pdb and amber's parameters.
Then I do a single point calculation to get the potential energy. I am using mdin like: cat << EOF >| mdin Single point &cntrl imin=0, maxcyc=0, ntmin=2, ntb=0, igb=0, cut=999, / EOF Then I test the same input parameters with Namd2, using namd.conf: cat << EOF >| AAAamb_namd.conf outputEnergies 1 # Energy output frequency DCDfreq 1 # Trajectory file frequency timestep 2 # in unit of fs temperature 300 # Initial temp for velocity assignment cutoff 999 switching off # Turn off the switching functions PME off # Use PME for electrostatic calculation amber on # Specify this is AMBER force field parmfile AAAamb.prmtop # Input PARM file ambercoor AAAamb.inpcrd # Input coordinate file outputname AAAamb # Prefix of output files exclude scaled1-4 1-4scaling 0.833333 # =1/1.2, default is 1.0 minimize 0 EOF I have only a 0.001 kcal/mol absolute diff (or relative 0.0037%) for the Elec term, everything else is absolutely the same. Then comes gromacs. I convert my prmtop and inpcrd to gromcs top and gro with either acpype or amb2gmx and then doing a single point with file: cat << EOF >| SPE.mdp integrator = md nsteps = 0 dt = 0.001 constraints = none emtol = 10.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no nstlog = 1 nstenergy = 1 nstvout = 1 nstfout = 1 nstxtcout = 1 comm_mode = ANGULAR EOF Converting gromacs energies (kJ/mol) by dividing the terms by 4.184 and they don't match amber/namd results. See relative diffs (abs(g-a)/max(abs(a),abs(g))): Bond: 5.87% Angle: 3.49% Dihe: 0.14% vdW: 0.52% Elec: 0.17% Pot.Tot: 5.90% I am very surprised to find this difference, in special for Bond since it's for this term essentially the same equation and parameters. Any ideas of what could be missing here? Many thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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