[gmx-users] Fwd: using nopbc is not equal to using pbc with big box dimensions

[Mark Abraham]

... if 0.7nm cut-offs are meaningfully large for the system in question.

Mark


On Tue, Dec 3, 2013 at 9:28 AM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> So, remove PME in the large box case and everything must be nice.
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Tue, Dec 3, 2013 at 2:14 AM, Golshan Hejazi <golshan.hejazi at yahoo.com>
> wrote:
> > Thanks for your reply. The result is surprisingly different:
> >
> > with nopbc            Potential energy=       -2.53730634908684e+05
> > with large box        Potential energy=  -2.21066633251456e+05
> >
> > I have tried with very large boxes too! but results are not even similar.
> > This is what I am using as input in mdp file:
> > pbc                        = no
> > nstlist                     = 0
> > epsilon_r                = 1.
> > ns_type                  = Simple
> > coulombtype          = Cut-off
> > vdwtype                 = Cut-off
> > fourierspacing        = 0.12
> > ; EWALD/PME/PPPM parameters
> > pme_order             = 4
> > ewald_rtol              = 1e-05
> > epsilon_surface      = 0
> > optimize_fft            = yes
> > rlist                        = 0.
> > rcoulomb               = 0.
> > rvdw                      = 0.
> > emtol                     = 1.0
> >
> > And this is for when I use the large box:
> > pbc                       = xyz
> > nstlist                   = 10
> > epsilon_r              = 1.
> > ns_type                = grid
> > coulombtype         = pme
> > vdwtype                  = Cut-off
> > fourierspacing           = 0.12
> > ; EWALD/PME/PPPM parameters
> > pme_order                = 4
> > ewald_rtol               = 1e-05
> > epsilon_surface          = 0
> > optimize_fft             = yes
> > rlist                         = 0.7
> > rcoulomb                 = 0.7
> > rvdw                       = 0.7
> > emtol                     = 1.0
> >
> >
> >
> > On Monday, December 2, 2013 7:45 PM, Dr. Vitaly Chaban <
> vvchaban at gmail.com>
> > wrote:
> > The fact that images are separated by a distance exceeding the cutoff,
> > does not mean that they do not interact electrostatically.
> >
> > I hope the results are not much different...
> >
> >
> > Dr. Vitaly V. Chaban
> >
> >
> >>
> >> On Mon, Dec 2, 2013 at 11:46 PM, Golshan Hejazi
> >> <golshan.hejazi at yahoo.com>wrote:
> >>
> >>> Hello,
> >>>
> >>> I would like to compute the energy of a system in vacuum. For this I
> >>> first
> >>> computed energy by using nopbc and putting rculomb=rvdw=0 ...
> >>> Then I computed the energy using pbc with a big box dimension (periodic
> >>> images are separated by a length more than cutoff )... this means that
> >>> periodic images dont interact ... results are different ... but which
> one
> >>> is correct?
> >>>
> >>>
> >>> Can you help me to understand this better
> >>> G.
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