Thank you for the references, Jiri.
I'll test things with the benchmark case and see how it looks.
In my system, I did add 30 sodium ions to neutralize the backbone
charges, prior to solvation. In this case, it's roughly equivalent to a
5 mM sodium phosphate concentration (the paper mentions 10 mM).
Do you think I should artificially increase the number of added ions
(say, to 60), or should I use packmol to explicitly add sodium and
phosphate ions to match the 10 mM concentration? Would you expect any
difference from these two approaches? Or should I just add the
equivalent of 150 mM of Na+ with packmol?
Thanks again
Sasha
Jiri Sponer wrote:
> common net neutralizing should work for RNA, would be around 0.1-0.2 M,
>
> If no ions added, then it would be unstable.
>
> Jiri
>
>
>
>> did you include the salt used in the experiment?
>>
>> On Fri, Oct 15, 2010 at 6:08 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>>
>>
>>> Hi all,
>>> I've been trying to reproduce a structure of a hairpin-folded RNA
>>> fragment starting from an experimentally determined NMR structure (PDB
>>> id 1JO7). However, it keeps rapidly unwinding retaining only the base
>>> pairing, but not the tertiary structure. Typically, it takes only
>>> several ns to severely unwind. I have tried a variety of input
>>> parameters, but with little success. The latest input files are given
>>> below the message.
>>>
>>> The last force field I used was ff99bsc0 with counterions added and
>>> solvated with TIP3P water in a box with 14 A margins. I also tried
>>> restraining several bases at the cutoff point (where the rest of the
>>> full RNA would be), but with no positive effect on the conformation of
>>> the hairpin.
>>>
>>> Could you please take a look at the input files in case there is
>>> something's not right there?
>>> At this point, there are three possibilities:
>>> 1. Something is wrong with input, solvation, etc. (i.e. my fault)
>>> 2. The force field is inadequate for this problem
>>> 3. The published structure is physiologically irrelevant, and thus
>>> cannot be reproduced in a stable simulation.
>>>
>>>
>>> I would very much appreciate any advice.
>>>
>>> Thanks
>>>
>>> Sasha
>>>
>>>
>>>
>>> Minimization 1
>>> &cntrl
>>> imin = 1,
>>> maxcyc = 10000,
>>> ncyc = 5000,
>>> ntb = 1,
>>> ntr = 1,
>>> cut = 15
>>> /
>>> Hold the solute fixed
>>> 500.0
>>> RES 1 31
>>> END
>>> END
>>>
>>> Initial minimization whole system
>>> &cntrl
>>> imin = 1,
>>> maxcyc = 10000,
>>> ncyc = 5000,
>>> ntb = 1,
>>> ntr = 0,
>>> cut = 15
>>> /
>>>
>>> Heating
>>> &cntrl
>>> imin = 0,
>>> irest = 0,
>>> ntx = 1,
>>> ntb = 1,
>>> cut = 20,
>>> ntr = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> tempi = 0.0,
>>> temp0 = 300.0,
>>> ntt = 3,
>>> gamma_ln = 2.0,
>>> nstlim = 25000, dt = 0.001,
>>> ntpr = 250, ntwx = 250, ntwr = 1000
>>> /
>>> Keep solute fixed with weak restraints
>>> 10.0
>>> RES 1 31
>>> END
>>> END
>>>
>>> Density equilibration
>>> &cntrl
>>> imin = 0,
>>> irest = 1,
>>> ntx = 5,
>>> ntb = 2,
>>> cut = 15,
>>> ntr = 1,
>>> ntp = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> temp0 = 300.0,
>>> ntt = 3,
>>> gamma_ln = 2.0,
>>> nstlim = 25000, dt = 0.001,
>>> ntpr = 250, ntwx = 250, ntwr = 1000
>>> /
>>> Keep solute fixed with weak restraints
>>> 10.0
>>> RES 1 31
>>> END
>>> END
>>>
>>>
>>> First equilibration with some restraints on the solute
>>> &cntrl
>>> imin = 0,
>>> irest = 1,
>>> ntx = 5,
>>> ntb = 2,
>>> cut = 12,
>>> ntp = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> ntr = 1,
>>> taup = 2.0,
>>> temp0 = 300.0,
>>> ntt = 3,
>>> tol = 0.000001,
>>> gamma_ln = 2.0,
>>> nstlim = 2000000, dt = 0.001,
>>> ntpr = 10000, ntwx = 10000
>>> /
>>> Set
>>> 10.0
>>> FIND
>>> * * B *
>>> SEARCH
>>> RES 1 31
>>> END
>>> END
>>>
>>>
>>> Full equilibration
>>> &cntrl
>>> imin = 0,
>>> irest = 1,
>>> ntx = 5,
>>> ntb = 2,
>>> cut = 12,
>>> ntp = 1,
>>> ntc = 2,
>>> ntf = 2,
>>> ntr = 0,
>>> taup = 2.0,
>>> temp0 = 300.0,
>>> ntt = 3,
>>> tol = 0.000001,
>>> gamma_ln = 2.0,
>>> nstlim = 2000000, dt = 0.001,
>>> ntpr = 10000, ntwx = 10000
>>> /
>>>
>>>
>>>
>>> Production simulation (500 ps run - one of many)
>>> &cntrl
>>> imin = 0, irest = 1, ntx = 7,
>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>> taup = 2.0,
>>> cut = 10, ntr = 0,
>>> ntc = 2, ntf = 2,
>>> temp0 = 300.0,
>>> ntt = 3, gamma_ln = 2.0,
>>> nstlim = 250000, dt = 0.002,
>>> ntpr = 500, ntwx = 500, ntwr = 250000
>>> /
>>>
>>>
>>>
>>>
>>>
>>>
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Received on Fri Oct 15 2010 - 17:00:04 PDT
