[gmx-users] Reg: Energy minimisation of hexane

[vinothkumar mohanakrishnan]

Hi Mark

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?.

Regards
Vinoth

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.
>
> Mark
>
>
> > 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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