Hi,
OK, maybe dialanine is smaller than things you've already tested (though it
is surprisingly challenging, as you will see in the enhanced-sampling
literature). Perhaps you can estimate from your CG work how many
independent samples you need for a converged simulation as a function of
Hi Mark,
Thank you very much for your answer.
The main problem is that there is no previous literature because this is a
new integration methodology that we are developing. I have tested my
methods in a coarse-grained toy system and I was trying to do something
similar in a more realistic system.
Hi,
I do not think it is sensible to attempt to measure the relative efficiency
of two different methods in the absence of evidence that either has sampled
approximately ergodically. This is why many approaches to enhance sampling
start testing with toy systems like alanine dipeptide. You should
Dear all,
Due to the computational facilities that I can use I am running 5000 ps
simulations with the villin headpiece system and I am trying to compare the
sampling efficiency of two different methods.
Since for this short simulations, I am not able to observe the folding
phenomena, what would
