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

[Richard Broadbent]

PME is stands for Particle Mesh Ewald. Ewald summation is a way to 
calculate the energy of an infinite lattice of infinitely ranged 
potentials. The reason for using PME is to include the effect of all the 
pbc images in your simulation, without this (or an equivalent technique) 
for long range potentials in periodic systems such as coulomb 
interactions you will get the wrong answer.

With regards to simulating a system in vacuum, if you do not want to 
include interactions with periodic images why would you put periodic 
images in your simulation?

Also as Mark pointed out why are you using a cut-off radius of 0.7nm I 
don't know any force field which uses such a cut-off.

Richard


On 03/12/13 14:17, Golshan Hejazi wrote:
> I think I am confused. There are two things that i dont
>
> When we use PME with the very large box. System should not interact with its periodic images. right? This means that I can compute the energy of the system as it is in the vacuum. Now, lets say that I use nopbc option and I get another value and very different for the energy.
>
> When they are different and in both cases there is not interaction with pbc images, means that the way that electrostatic is computed for the system itself is different. right?
>
> SO, Which one should someone rely on?
>
> Which way to report a energy for a system in vacuum?
>
> Thanks for your help guys
> G.
>
>
>
> On Tuesday, December 3, 2013 3:27 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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