Dear all,
I have a molecule consist of 81 atoms in vacume and I want to calculate the
normal modes of it. The first conjgrad minimization is done successfully
but in Newton-Raphson after the first step the energy goes to infinity.
Does Anyone have any idea what the problem can be? Following you can see
the input and output.
Best regards,
Meisam
Input:
--------------------------------------------------------
m = getpdb("res478_min.pdb");
allocate m_xyz[3*m.natoms];
allocate f_xyz[3*m.natoms];
readparm(m, "res478.prmtop");
mm_options("cut=100.0, ntpr=50, nsnb=20, gb=0, diel=C");
mme_init(m, NULL, "::ZZZZ", m_xyz, NULL);
// Do some conjugate gradients.
dgrad = 0.005;
setxyz_from_mol( m, NULL, m_xyz );
ier = conjgrad(m_xyz, 3*m.natoms, fret, mme, dgrad, 1.0, 20000);
// Do some Newton-Raphson.
mm_options("ntpr=1");
dgrad = 1.e-12;
ier = newton(m_xyz, 3*m.natoms, fret, mme,mme2, dgrad, 0.0, 100);
// get the normal modes:
ier = nmode( m_xyz, 3*m.natoms,mme2, 20,0,0,0,0);
-------------------------------------------------------------------------------------
Output:
------------------------------------------------------------
ff: 850 33.21 94.24 -7.01 -54.03 0.00 0.00
3.35e-04
nblist_box, number of atoms= 81
nblist_box, number of pairs= 2813
nblist_box, number of atoms= 81
nblist_box, number of pairs= 2813
nblist_box, number of atoms= 81
nblist_box, number of pairs= 2813
ff: 900 33.21 94.24 -7.01 -54.03 0.00 0.00
1.92e-04
mm_options: ntpr=1
ff: 1 33.21 94.24 -7.01 -54.03 0.00 0.00
9.75e-05
iter Total bad vdW elect nonpolar genBorn
frms
ff: 1 59.45 94.24 6.77 -41.57 0.00 0.00
2.89e+00
adding 0.00000 to diagonal of the hessian
rms of search direction: 2.8930276
For alpha = 0.00000 energy = 33.2060564657
For alpha = 1.00000 energy = 139971511.6351643801
For alpha = 2.00000 energy = 38801567206756.8046875000
For alpha = 4.00000 energy = 45377266.0887722522
For alpha = 2.68690 energy = 20152302.1785228439
For alpha = 2.25044 energy = 38466135.0552254021
For alpha = 2.41112 energy = 16404091.9306907263
For alpha = 2.32573 energy = 16779390.1586112827
ff: 2 16779390.16 14942430.46 1836808.68 151.02 0.00 0.00
2.21e+06
ff: 2 14949263.70 14942430.46 6826.94 6.30 0.00 0.00
2.18e+04
---------------------------------------------------------------------------------------------------
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Received on Tue Nov 05 2013 - 02:30:03 PST
