[gmx-users] Re: high repulsion in packed system

[Vitaly Chaban]

Dear Moeed:

1. You have to avoid unphysical energies. To achieve this, please
enlarge the unit cell, so that your particles do not intersect in the
initial configuration.
2. Then NPT MD is used to compress the system to its smaller size (as
you need). Please select a pressure that is big enough for this. Maybe
1 bar, or maybe 100 bar - this depends on your particular system, its
nature and the degree of compression you want.
3. Then if you want NVT, correct the box size in conf.gro, so it
corresponds to the density of interest.

The only purpose of my suggestions is to evoid explosion at start. On
the other part, you may also try to enlarge "emstep" in the EM - and
it will be hopefully more successful  than you report earlier.

Cheers,
Dr. Vitaly Chaban


>
> Dear Dr Chaban,
>
> Thanks for your reply. If I do NPT to compress the box to the initial size
> (small) EM works perfectly ?
>
> I dont exactly realize the justification behind what you said. You mean I
> have to change the pressure in mdp file which gives the box size I want?
>
> Later, I need to perform actual NPT and NVT simulations with this packed
> system. Can I not do NVT with this density?
>
> Thanks,
> Moeed
>
> In "PE60-3.75nm3.gro" enlarge the box size. Then use NPT simulation to
> compress the MD box.