[gmx-users] about soft core potentials and very high VdW

[Tsjerk Wassenaar]

Hi John,

If you explain a bit more of what you're trying and how that resulted in
these overlaps, maybe someone can provide more adequate help.

Cheers,

Tsjerk


On Sat, Feb 1, 2014 at 1:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/31/14, 6:42 PM, jhon michael espinosa duran wrote:
>
>> Hi guys
>>
>> Can I use softcore potentials during the minimization?
>> the reason to do so is because my initial system has many non-bonded
>> atoms overlapping, so during energy minimization the energy is too high
>> (infinite) so after a couple of iterations is finished with the argument of
>> reaching machine numerical converge, but in fact nothing happen.
>> And If I star the simulation with the system in such conditions it just
>> explodes.
>>
>>
> Worth a shot, but if you've got so many bad clashes that it's necessary,
> I'd suspect there has to be some better way of constructing the system.
>  I'd try applying the softening to all nonbonded interactions, not just van
> der Waals via soft-core potential; using the free energy options with the
> whole system coupled, along with a suitable lambda value, could be helpful.
>  You could also wind up with a completely distorted structure, though.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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> University of Maryland, Baltimore
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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-- 
Tsjerk A. Wassenaar, Ph.D.