From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Aug 29 2012 - 15:37:06 CDT
Thomas Albers <talbers_at_binghamton.edu> writes:
> Date: Wed, 29 Aug 2012 16:06:04 -0400
> From: Thomas Albers <talbers_at_binghamton.edu>
> To: Namd Mailing List <namd-l_at_ks.uiuc.edu>
> Subject: namd-l: Accelerated MD
> Does anyone on this list perhaps have experience with accelerated MD?
> We are looking at a short peptide in a membrane (30000 atoms total)
> and are trying to find suitable values for E and alpha in dual-boost
> Here are the relevant average energies (kcal/mol) for classical MD:
> dihedral 4070.72, total -42381.53
> With accelerated MD we see:
> dihedral 6362.78, total -40156.92
> The dihedral energy is higher, as expected, because the system
> explores a greater amount of phase space, but it seems that the
> contribution to the increase in total energy comes almost exclusively
> from the dihedral energy. If I read this right there is almost no
> boost at all applied to the diffusive degrees of freedom. Am I
> understanding the data right?
What E and alpha values did you use? Which equation did you use to
determine these E and alpha values?
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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