[gmx-users] Simulation parameter problem about protein unfolding
amethyst0 at 126.com
Mon Oct 18 15:45:46 CEST 2010
This information is helpful!
I think I need to deal with the simulation result really carefully. Thanks for the help! And also thanks Massimo for the information about expected gyration radius of a purely non-interacting random chain!
At 2010-10-18 21:01:23，chris.neale at utoronto.ca wrote:
>to answer this, please see David's post and my reply. To answer if
>your unfolded state ensemble is accurate, you will need to know some
>experimentally evaluated quantities of the state that you are trying
>to reproduce: 498K, 26 atm, a certain amount of salt, etc, (but not
>including the forcefield model or cutoffs, which are obviously
>intrinsically part of the model).
>Then, if your data does not match this, then you can conclude that the
>simulation time was too short or the parameters were not valid. Also,
>I guarantee it was... you'll probably need something more like 10 ms -
>10 s (what is the unfolding rate under these conditions?), which is
>rather difficult to obtain).
>Comparing a temperature denatured state to an AFM denatured state, one
>does not expect them to match. The point here was to ask: are you sure
>that your ensemble of conformations is incorrect given the conditions?
>-- original message --
>> At 2010-10-18 12:56:31£¬chris.neale at utoronto.ca wrote:
>> Generally, forcefields are not parameterized for temperatures other
>> than 298K, so simulations are not expected to reproduce the expected
>> properties (like boiling water and the correct temperature
>> denaturation of proteins).
>> There's almost certainly other issues here (including the fact that
>> I'm entirely sure that you can get a lot more than 24 ns of
>> simulation on a 54 aa protein; and 26 atom of pressure seems pretty
>> arbitrary) but it will come down to this eventually.
>> Just because you found a paper in which they get a denatured state
>> does not imply that they got the correct denatured state.
>Hi, Chris! Thanks for the reply! I have not conducted unfolding
>before, so I compared my result with other's to make sure it is reasonable in
>some extend. The 26 atm pressure comes from experiment result (Haar et al.,
>1984) mentioned in some MD related papers (e.g. 'J. Mol. Biol. (2000) 296,
> I've searched the maillist
>and noticed some issues about High temperature simulations. I'm not sure
>whether the 'ilmm' force field has been optimized for high temperature
>simulation. I also noticed some users asked about MD parameters in
>protein'. And the parameters they used are different from ours' (e.g. the
>'rlist', 'rcoulomb' and 'temperature or pressure couple algorithm').
> I just want to make sure I
>didn't make mistakes in these parameters which maybe cause the protein keeping
>in a compact state! The radius of gyration of the protein fluctuated around
>1.1nm (never bigger than 1.4nm) during our 30ns simulation now. If the MD
>parameters I chose have no problem, then I could keep going. Any comment?
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