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.
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
---------------------------------------------------------------------------------------------------
Best regards,
Meisam
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Received on Tue Nov 05 2013 - 01:00:03 PST
