After energy minimzation, I visualized the pdb and all atoms are really far from each other.
NIlesh On Thu, May 27, 2010 1:10 pm, Erik Marklund wrote: > Bonds don't break in gromacs without qm/mm ...yet. Why do you think > they're broken? > > Erik > > > Nilesh Dhumal skrev: > >> 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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > [email protected] http://folding.bmc.uu.se/ > > -- > gmx-users mailing list [email protected] > 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 [email protected]. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
