Hii,
I was trying to calculate the normal modes of a Carbon dioxide
molecule solvated in TIP3P water molecules. I have used the following input
file
*molecule m;*
*float x[5931], fret;*
*float m_xyz[ dynamic ], f_xyz[ dynamic ], v[ dynamic ];*
*readparm(m, "co2.prmtop");*
*allocate m_xyz[ 3*m.natoms ];*
*allocate f_xyz[ 3*m.natoms ];*
*allocate v[ 3*m.natoms ];*
*mm_options( "cut=8., ntpr=50, nsnb=9999" );*
*mme_init ( m, NULL, "::ZZZ", x, NULL);*
*setxyz_from_mol (m, NULL, x);*
*// conjugate gradient minimization*
*conjgrad (x, 3*m.natoms, fret, mme, 0.1, 0.001, 2000);*
*//Newton-Raphson minimization \fP*
*mm_options ( "ntpr=1");*
*newton(x, 3*m.natoms, fret, mme, mme2, 0.0000001, 0.0, 6);*
*//get the normal modes:*
*nmode(x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);*
Total number of atoms in the system is 5931. I am getting following error
during execution of the nab script.
*Reading parm file (co2.prmtop)*
*title:*
*default_name
*
* Parameter topology includes 10-12 terms:*
* These are assumed to be zero here (e.g. from TIP3P water)*
*Segmentation fault (core dumped)*
Please help me fixing the issue.
Thanks and regards
Sanjib Paul
~
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Received on Mon Mar 28 2016 - 07:30:03 PDT
