From: Gianluca Interlandi (
Date: Fri May 20 2016 - 22:09:16 CDT

Dear list,

I am about to purchase a new workstation for trajectory analysis. I am
to decide between the following two prcessors:

E5-2620 v3 E5-2623 v3
Cores 6 4
Freq 2.4 GHz 3.0 GHz
Cache 15 MB 10 MB
Cost + 50$

I wonder whether the higher clock rate of the E5-2623 justifies having a
smaller number of cores and smaller cache. Do the additional 0.6 GHz
into a significant speed increase when post-processing a trajectory with
e.g. RSMD, energy evaluation, surface analysis, etc.? According to, the higher clock frequency brings a speed increase of only
8-9% when comparing single thread.

Also, does the L3 cache matter for VMD/NAMD?



Gianluca Interlandi, PhD
                    +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.