On Mon, Sep 1, 2014 at 7:38 AM, Asmita Gupta <asmita4des.gmail.com> wrote:
> But, then i have 3 different runs for the same system, each 200ns. Is it
> incorrect to say that the system has experienced conformational sampling
> for a total of 600ns, which might be long enough for loops?
Yes, that is incorrect because each simulation is independent. The
fact that you did not observe the flip in your third simulation means
at the very least you need to run this simulation longer, as Dave
suggested. One thing you could do would be to look at the
distributions for the zeta, chi, and delta torsions from each
independent simulation. If you don't have good overlap between
distributions from independent simulations then these aspects of the
system are not well converged and you should probably run them longer.
-Dan
>
> Asmita
>
>
> On Mon, Sep 1, 2014 at 5:54 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Mon, Sep 01, 2014, Asmita Gupta wrote:
>> >
>> > In 2 out of 3 trajectories, the structure is experiencing a loop residue
>> > backbone flipping (zeta, chi and delta), after which it remains stable.
>> > However, with parmbsc0, this residue flipping is not observed at all,
>> > neither with YIL chi correction.
>>
>> One useful analysis is to see how long it took for the flip to take place
>> in
>> the two trajectories where it did happen. If these are significant
>> fractions
>> of the 200 ns length, then it is plausibly just a matter of chance that you
>> did not see such behavior in the third run. You could extend the third run
>> longer to see what happens.
>>
>> >
>> > is 200ns enough for a good conformational sampling?
>>
>> This is not sufficient in general to sample RNA loop configurations.
>>
>> ....dac
>>
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Mon Sep 01 2014 - 08:00:03 PDT
