[gmx-users] box size and neighbor list cut-off

Johnny Lu johnny.lu128 at gmail.com
Mon Aug 17 23:07:43 CEST 2015

Thank you for the advices.

I tried setting different varlet buffer drift in the 1st equilibration run
(nvt) for 5 seconds.
>From the log file of mdrun, I get:

rlist        verlet-buffer-drift
1.09        0.000005
1.114        0.0000005
1.135        0.00000005 <=

1.173        0.0000000005
1.234        0.00000000000005
1.284        0.000000000000000005

Are these numbers real?

The wiki says the constraints already causes 0.0001kj/mol/atom in single
precision gmx mdrun.

If I use double precision gmx mdrun and constraint h-bonds, can I expect
1.135 rlist to give a verlet-buffer-drift as small as the one in the table?

Thank you again.

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