[gmx-users] Re: System size and minimum image convention

[Dr. Vitaly Chaban]

I mean the number of balls which interact in your unit box. If your
system is composed of atoms, than it is atoms. If you have
coarse-grained representation of virtual sites, it is a total number
of them.

Dr. Vitaly Chaban


On Sat, Feb 23, 2013 at 8:23 AM, Elisabeth <katesedate at gmail.com> wrote:
> Hi Vitaly,
>
> When you say interaction site you mean number of atoms in the box? How one
> can obtain the interaction sites?
>
> Thanks
>
> On 22 February 2013 05:04, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
>>
>> >why for a binary
>> > (solute+solvent) the size should be larger than 2 Rc? I thought minimum
>> > image convention works for all atoms (solute ans solvent) and this makes
>> > sure forces are not double-counted. What if the solute is a polymer, I
>> > mean
>> > how can one calculate diameter of a long chain?
>>
>>
>> If the box size is NOT larger than 2Rc than Rc is larger than a half
>> of the box. If it is larger than a half of the box than minimum image
>> convention cannot work.
>>
>> This is not a good idea to use so small box. You will end up with
>> methodological problems of some kind eventually.
>>
>>
>> Dr. Vitaly Chaban