Hello, I am trying to calculate the normal vibrational spectra of glcuose molecule in vaccum. After the energy minimization, I found all the bonds are broken. I have pasted the input file for energy minimzation. WHy all bonds are geting broken. Nilesh
define = -DFLEXIBLE constraints = all-bonds integrator = L-BFGS nsteps = 15000 nbfgscorr = 50 emtol = .001 emstep = 0.1 gen_vel = yes gen-temp = 300 nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist =10 ; ns algorithm (simple or grid) ns-type = simple ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist = 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field ; Method for doing Van der Waals vdw-type = Cut-off ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = no ; nblist cut-off rlist = 0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-Off rcoulomb-switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field ; Method for doing Van der Waals vdw-type = Cut-off -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
