[CP2K:5452] Re: Monte carlo simulations

[sajid iqbal]

Hi Matt,

Thank you for response. I spend whole month to figure out the error and i
cant. I can work with all protein structures without any problem but when i
try to use coordinates input file for RNA/DNA using nucleic acid builder it
did not work and gives me error in coordinate file. If you have towhee
experience then I can forward you my files if you can help me. I wrote to
towhee users and developer team as well but did not hear any thing.

thank you again!


On Thu, Jun 12, 2014 at 10:22 PM, Matt McGrath <obfis... at gmail.com> wrote:

> 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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