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

[Johnny Lu]

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

On Mon, Aug 17, 2015 at 5:07 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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.
> (
> http://www.gromacs.org/Documentation/Cut-off_schemes#How_to_use_the_Verlet_scheme
> )
>
> 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.
>