[gmx-users] Velocity ACF not decaying to zero

Vasilii Artyukhov darth.vasya at gmail.com
Thu Jul 10 22:24:17 CEST 2008

Dear all,

I'm trying to compare the diffusion constants resulting from g_msd -mol and
g_velacc -mol -nonormalize. The agreement for pure water (512 molecules, 300
K) seems fine (g_analyze output of g_velacc falls into the +- interval of
g_msd), but for a more complex system (4000 waters + 80 small solutes, 290
K), the resulting velocity ACF decays to a nonzero value. This might result
from COM motion, but I think I'm removing it:

; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1

Any hints on what this might mean?

Best regards,
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