Monte carlo simulations

[Matt McGrath]

Hi,

In theory, you can run this simulation with CP2K.  In practice, though, you 
will never get a molecule as big as RNA to swap between the boxes, so it 
would not be helpful at all.  MCCCS Towhee is a much better choice for 
several reasons in this case, in part because it has significantly better 
conformational sampling (both in a box and between boxes), and two because 
it will be much faster with a classical forcefield (after a move it only 
recalculates the interactions which have changed when using a pairwise 
potential, as opposed to recalculating everything).  So I would try to fix 
the problem with MCCCS instead of trying to use CP2K in this case.

                                   Cheers, Matt 

On Thursday, June 12, 2014 6:20:23 AM UTC+2, sajid iqbal wrote:
>
> Dear Users, 
>
> I want to run MC simulations to calculate the single step energies. I want 
> to set up two boxes and put one RNA molecule in box1 using pdb file and put 
> fixed number of polyethylene molecules in box2. I want to move RNA molecule 
> from box1 to box2 and calculate the energy of box2 or just RNA in box2 at 
> fix temp and pressure. Can I run this kind of calculations and how ? Any 
> idea would be great help.
>
> I tried MCCCS towhee but there is always error with coords file. if 
> someone needs more details i can provide. 
>
> Thank you very much
>
>
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