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，[email protected] wrote: >Chen, > >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? > >Chris. > >-- 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, >1257-1282'). > > 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? > > > >-- >gmx-users mailing list [email protected] >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [email protected]. >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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