[gmx-users] regarding 2002 post showing protein unfolding with long timesteps

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Aug 21 18:12:02 CEST 2008

David van der Spoel, can you please comment on this post of your from 2002:

"long timesteps combined with dummies give me unfolding proteins while without
dummies and 2 fs the systems are stable. These are long-time effects (i.e.
after a couple of ns things start to happen). I have to do more test
before I can conclude anything."

reference: http://www.gromacs.org/pipermail/gmx-users/2002-July/002171.html

I searched your name with the work timestep and looked through the  
~200 titles of posts, but couldn't find anything.

I am currently considering a 5fs timestep and, even though it is  
nicely described in the gromacs 4 paper, I wanted to ensure that  
whatever problem you might have been experiencing is now solved.  
Alternatively, if it was a particular type of system that appears to  
be refractory to the 5fs timestep options (properly instituted with  
dummies, etc) then that information would also be valuable to me.

My usage will be for free energy calculations of a protein in a lipid  
bilayer so obtaining information on the dynamic processes is not  
important to me here.


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