[gmx-users] vibrational spectra of glucose

[Mark Abraham]

----- Original Message -----
From: Nilesh Dhumal <ndhumal at andrew.cmu.edu>
Date: Tuesday, June 1, 2010 10:37
Subject: [gmx-users] vibrational spectra of glucose
To: gmx-users at gromacs.org

> Hello,
> 
> I want to  calculate the normal vibrational spectra of PF6 anion.
>  After the energy minimization, I found that the structure 
> has lost his
> symmetry. It does not have Oh symetry.  I compared this 

That's normal. QM codes go to great lengths to recognize symmetry and use it because it makes the calculation quicker. MD codes don't bother, because they don't get used for systems with such high symmetry.

> structre with
> ab-initio which is not matching.
> I have pasted the input file for energy minimzation.
> WHy structure is loosing its symmetry or why its not giving 
> proper local
> minima.

It'll "lose" symmetry if it didn't have it to start with (so you'll need the axes to line up with F-P-F vectors), or if the force field is assymetric.

I don't know of any force field that would claim to support parameters for PF6 anion, but presumably you've done your homework there. If so, the documentation there should mention how they ran it.

This looks like a much easier problem for a QM code to solve - B3LYP/6-31G* is probably better than any MM parameterization, and with high symmetry, maybe quicker too!

Mark

> define                   = -DFLEXIBLE
> 
> constraints              = none
> 
> integrator               = L-BFGS
> 
> nsteps                   = 50000
> 
> nbfgscorr                = 50
> 
> emtol                    = 0.0001
> 
> emstep                   = 0.0001
> 
> 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
> 
> ; cut-off lengths
> 
> 
> rvdw-
> switch              = 0
> 
> rvdw                     = 0
> 
> 
> 
> 
> 
> 
> 
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php