AMBER Archive (2005)

Subject: Re: AMBER: Dummy Atom Types on both states

From: Julien Michel (j.michel_at_soton.ac.uk)
Date: Tue Feb 15 2005 - 10:10:34 CST


Hi,

If you have enough resources, you should run the same simulation different
times using different starting conformations/random seeds. You may however,
make the vexing discovery that the resulting set of free energies are
more spread than the hysteresis on a single run would have suggested ...

-- 
Julien Michel
University of Southampton
Department of Chemistry
Dr J. W. Essex group 

> Hello, > I have a relevant question. Since dummy atoms can only be in one state > (lambda = 1), if we want to estimate the error of free energy calculation, > should we use different starting conformations to redo the calculation, > instead of doing in the "forward" and "reverse" direction? > Thank you very much! > Yipin ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu