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

[Justin Lemkul]

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
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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