[AMBER-Developers] mme and mme2 energies are different

From: InSuk Joung <i.joung.gmail.com>
Date: Sat, 14 Aug 2010 22:15:09 -0400

I have two different energies from mme and mme2 routines of NAB. Here is
the nab code:

molecule m;
int num, ier, i;
float m_xyz[dynamic], f_xyz[dynamic];
float dgrad, fret;

m = getpdb( argv[2] );
allocate m_xyz[3*m.natoms];
allocate f_xyz[3*m.natoms];
//allocate h_xyz[3*m.natoms];
//allocate mass[m.natoms];

readparm(m, argv[3]);

for ( i = 1; i <= m.natoms*3; i++ ) {
    m_xyz[i] = atof( argv[i+3] );

// Energy
mm_options("cut=999.0, ntpr=1, nsnb=999, gb=0");
mme_init(m, NULL, "::ZZZZ", m_xyz, NULL);

fret = mme( m_xyz, f_xyz, -1 );
printf( "mme returns %.60e\n", fret );

// get the normal modes:
ier = nmode( m_xyz, 3*m.natoms,mme2, num ,0,0.0,0.0,0);
  printf("nmode returns %d\n", ier );


This is the output of the energy evaluation:

-- Parameter topology includes 10-12 terms:
     These are assumed to be zero here (e.g. from TIP3P water)
    mm_options: cut=999.0
    mm_options: ntpr=1
    mm_options: nsnb=999
    mm_options: gb=0
     bond: 5.455061285
    angle: 0.531769495
 dihedral: 0.204893077
    enb14: -0.500399875
    eel14: -1576.959704503
      enb: 14.870758041
      eel: 984.019892601
      egb: 0.000000000
    econs: 0.000000000
    esurf: 0.000000000
    Total: -572.377729879
     frms: 6.712036879
mme returns
      iter Total bad vdW elect nonpolar genBorn
ff: 1 -571.49 7.08 14.37 -592.94 0.00 0.00

Energy = -5.7148548010e+02
RMS gradient = 6.8996841060e+00
dysev time = 0.04 seconds

nmode analysis shows the energy evaluation at the beginning but the number
is different. Electrostatic and vdW energies seem to be the same but bonded
energies are different. I don't know which part of the energy makes the
difference. Could anybody tell me how to printout detailed decomposed
energies using mme2 routine? It looks like mme2 takes more than 5 arguments
which are more than the arguments described in AmberTools manual.

InSuk Joung
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Received on Sat Aug 14 2010 - 19:30:03 PDT
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