Dear all developers and users.
I conducted LMOD minimization using NAB program.(Ambertools 1.4, Amber11)
I want to get trajectory files from every optimization steps(lo.niter) of the script below.
According to Ambertools manual, trajectory is stored in lmod_traj[].
I think that I should use fopen(). but I don`t know how to use exactly.
Please help.
>script
allocate x[ 3*natm ]; allocate g[ 3*natm ];
setxyz_from_mol( mol, NULL, x );
xmin_opt_init( xo );
xo.maxiter = 100000;
xo.grms_tol = 0.05;
xo.method = 3;
xo.m_lbfgs = 3;
xo.print_level = 2;
mm_options( "ntpr=999, gb=1, rgbmax=999.0, cut=999.0, scee=1.0, scnb=1.0, diel=C");
mme_init( mol, NULL, "::ZZZ", dummy, NULL );
ene = mme( x, g, 0 );
ene = xmin( mme, natm, x, g, ene, grms, xo);
setmol_from_xyz( mol, NULL, x ); // load x[] into mol
fname = sprintf( "c2_gb1_ab_min.pdb" );
putpdb( fname, mol, "-nocid" ); // save conf in pdb file
lmod_opt_init( lo, xo ); // set up defaults
lo.niter = 30;
lo.nconf = 30;
lo.minim_grms = 0.1;
lo.nrotran_dof = 6;
lo.energy_window = 50.00;
lo.eig_recalc = lo.niter+1;
lo.ndim_arnoldi = 0;
lo.lmod_restart = 10;
lo.n_best_struct = 10;
lo.mc_option = 1;
lo.rtemp = 1.5;
lo.lmod_step_size_min = 1.0;
lo.lmod_step_size_max = 1.5;
lo.nof_lmod_steps = 0;
lo.lmod_relax_grms = 1.0;
lo.nlig = 0;
lo.print_level = 2;
xo.ls_maxatmov = 0.15;
allocate conflib[ lo.nconf * 3*natm ];
allocate lmod_traj[ (lo.niter+1) * 3*natm ];
mm_options( "ntpr=999, gb=1, cut=999.0, scee=1.0, scnb=1.0, diel=C" );
mme_init( mol, NULL, "::ZZZ", dummy, NULL );
Sangmin Lee
Yonsei University
KOREA
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Received on Thu Oct 04 2012 - 01:30:05 PDT
