[gmx-users] Water molecule can not be settled

[Mark Abraham]

Hi,

That looks strange, but VMD chooses its representations based on guesses
about atom names and distances, so it's quite possible to confuse it. I'd
look at VMD's console log to see whether it's complaining about anything.

Alternatively, the names and types are real and they're really that far
apart because that's what your model physics said. Find a single C-C bond
and measure its distance.

Mark

On Fri, Jul 1, 2016 at 11:25 AM zeineb SI CHAIB <zeineb-14 at hotmail.com>
wrote:

> Dear Mark,
>
> Again, thank you very much for your orientation.
>
> I suceeded in running a minimisation in vaccuo (just after pdb2gmx) with
> the following command line:
>
> gmx mdrun -ntmpi 1 -v -deffnm protein_invacuo -s protein_invacuo.tpr
>
> The mdp parameters were:
>
> integrator = steep
> nsteps = 1500
> emtol = 1000.0
> emstep = 0.01
> energygrps    = system
>
> pbc         = no
> nstlist = 0
> ns-type = simple
> rlist       = 0
>
> cutoff-scheme = group
> coulombtype              = cut-off
> rcoulomb                 = 0
> vdw-type                 = Cut-off
> rvdw                     = 0
>
> During minimisation, I had no error and Steepest Descents converged to
> Fmax < 1000 in 389 steps
> Potential Energy  = -8.8386008e+04
> Maximum force     =  9.7354883e+02 on atom 3974
> Norm of force     =  4.0786911e+01
>
> However,
>  when I visualised the .gro file generated after minimisation, in VMD,
> It can't correctly display the parametrized molecule (THF). For example,
>  for a representation in licorice, I had this (right and left are HEM
> and in the center is my THF!!):
>
> https://www.dropbox.com/s/xrxw473pywbiz1s/THG_problem.png?dl=0
>
> NB: my input structure has been obtained by homology modelling using
> MODELLER but I don't think that the problem is here because I already run
> an MD of 5ns with this structure but I added the topology of THF manually
> (like in bevanlab tutorial)!?
>
> What do you think happened?
>
> Regards.
>
> Zeineb
>
>
>
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