[gmx-users] Re: Have your ever got a real NVE simulation (good energy conservation) in gromacs?

[Szilárd Páll]

With the verlet cutoff scheme (new in 4.6) you get much better control
over the drift caused by (missed) short range interactions; you just
set a maximum allowed target drift and the buffer will be calculated
accordingly. Additionally, with the verlet scheme you are free to
tweak the neighbor search frequency (nstlist) to tune for performance.
As you anyway need a buffer, you should get similar if not better
performance as with the default group scheme with the added benefit of
and far better scalability - I.e. you'll be able to run the same
system on much larger number of cores.

For more details check the manual or the following wiki page:
http://www.gromacs.org/Documentation/Cut-off_schemes

Cheers,
--
Szilárd


On Fri, May 24, 2013 at 5:13 PM, cyberjhon <cyberjhon at hotmail.com> wrote:
> Hi Guys
>
> Thanks for your reply
>
> 1.  Ok guys I will use the following
>
> Double precision gromacs
>
> dt=1fs
> pbc                      = xyz
>
> nstlist                  = 5
> rlist                    = 1.7
> rlist_long               = 2.0
>
> coulombtype              = PME-Switch
> rcoulomb_switch       = 1.2
> rcoulomb                    = 1.4
>
> fourierspacing           = 0.12
> pme_order                = 6
> ewald_rtol               = 1e-5
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = yes
>
> vdw-type                     = Shift
> rvdw-switch                = 0
> rvdw                            = 1.7
>
> tcoupl                   = no
> pcoupl                   = no
>
> constraints              = h-bonds
> constraint-algorithm     = Lincs
> lincs-order              = 4
> lincs-warnangle          = 30
>
> 2. Any other suggestion ??
>
> Thanks
>
> John Michael
>
>
>
>
>
> --
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