I used the opls parameters in gromacs. NIlesh On Thu, May 27, 2010 1:17 pm, Erik Marklund wrote: > Where did you get the parameters for glucose? Those are my first > suspects. > > Erik > > > Nilesh Dhumal skrev: > >> 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 >>> >>> >>> >>> >>> >> >> >> > > > -- > ----------------------------------------------- > 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 > > >
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