[gmx-users] Reg: Energy minimisation of hexane
kmvinoth at gmail.com
Wed Oct 6 08:18:03 CEST 2010
I saw both the .gro file of hexane before and after EM in VMD as well
checked their coordinates. I am not able to make anything out of it. it will
better if one knows how to find the steric clash between two molecules?.
On Wed, Oct 6, 2010 at 11:08 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:
> ----- Original Message -----
> From: vinothkumar mohanakrishnan <kmvinoth at gmail.com>
> Date: Wednesday, October 6, 2010 15:20
> Subject: [gmx-users] Reg: Energy minimisation of hexane
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Hi all
> > I am trying to simulate 150 molecules of hexane in a triclinic box
> (8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from
> PRODRG and generated the topology using X2top command. when i run energy
> minimisation for hexane my potential energy is positve. is this right?. what
> i should correct to get the potential energy as negative. below is my
> result. any help is highly appreciated.
> > Steepest Descents converged to Fmax < 100 in 10454 steps
> > Potential Energy = 3.4133051e+04
> > Maximum force = 9.8812309e+01 on atom 635
> > Norm of force = 7.9230022e+00
> So something is unhappy, and the minimizer can't deal with it. Probably you
> have some massive steric clash, like two molecules overlying each other.
> Look at the contents of your simulation cell before and after EM.
> > Below is my contents of my em.mdp file
> > integrator = cg
> > emtol = 100.0
> > emstep = 0.01
> > nsteps = 50000
> > nstcgsteep = 1000
> > nstlist = 1
> > ns_type = grid
> > rlist = 1.0
> > coulombtype = PME
> > fourierspacing = 0.12
> > rcoulomb = 1.0
> > rvdw = 1.0
> > pbc = xyz
> > Regards
> > Vinoth
> > --
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