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

[Golshan Hejazi]

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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