Re: [ESPResSo] Bond Broken & NPT Simulations

[Jacob Kirkensgaard]

Hi Olaf

this is probably a stupid question, but how do you actually specify r_cut for 
the harmonic potential? From the documentation you can only specify the 
prefactor and the equlibrium bond length it seems. I use harmonic bonds  or 
FENE together with tabulated potentials where the cutoff is set by the maximal 
distance tabulated but does that influence the cutoff for the bonds? Is it set 
with the integrator or how?

thanks
jacob 

On Nov 19, 2009, at 9:31 AM, Olaf Lenz wrote:

> Hi!
> 
> Salvador Herrera Velarde wrote:
>> I ran my first simulations with skin = 0.4 and different number of 
>> processors [4,8,16], however,
>> due to the size of the system and the charges the simulation was very slow.  
>> So, I tried to increase
>> the number of processors to 32,64 but always I got the same message (Bond 
>> broken....) and the system crashes even during the thermalization (NVT + 
>> capped forces and No Electrostatics).
> 
> This is indeed the same as Jacob had, and the answer is the same as Axel gave 
> in
> http://fias.uni-frankfurt.de/pipermail/espresso/2009-November/000484.html
> 
> 
>> In my case the maximal range of interaction comes from the electrostatic 
>> interactions, and the cutoff radio is automatically optimized by ESPResSo 
>> using the command:
>> inter coulomb $bjerrum p3m tune accuracy $acc r_cut 0 mesh 0 cao 0
> 
> You stated above that there was no electrostatics during thermalization, and 
> it already happens there. Anyway: why do you think the rcut of the 
> electrostatics is the largest? Usually, rcut in that case is not very big, as 
> it is only the rcut of the short-ranged-part of the P3M algorithm. So I would 
> guess that it still helps to increase the size of rcut of the harmonic 
> potential.
> 
> Olaf
> 
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