[gmx-users] Simulation parameter problem about protein unfolding

Chen 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.
>> Chris.
>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  
>'unfolding a
>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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