[gmx-users] virtual site connected to dummy massive site

[Justin Lemkul]

On 11/26/17 12:34 PM, Faezeh Pousaneh wrote:
> Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
> question, I have no charges in systems on any atoms. So the extra DOF do
> not effect on potential.

Maybe I (and others) are missing something here. We understand there are 
no charges, but that only affects the Coulombic energies. The LJ 
potentials of two systems are only the same if the interacting species 
have the same configuration. Do your virtual particles interact with 
anything via LJ? If they don't, I don't understand their purpose. You 
have to do an apples-to-apples comparison.

-Justin

>
> Best regards
>
>
> On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Potential energy is a function of configuration. You can expect the same LJ
>> energy if you compare the same configuration, ie that the distribution of
>> states is identical. But if you would have the same total energy and a
>> different distribution between PE and KE (because the DOF change) then you
>> will not sample the same states.
>>
>> Mark
>>
>> On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <fpoosaneh at gmail.com>
>> wrote:
>>
>>> Dear Mark,
>>> thanks, but degrees of freedom goes to kinetic energies, still LJ
>> energies
>>> must be the same, yes?
>>>
>>>
>>> Best regards
>>>
>>>
>>> On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> Your systems have different available degrees of freedom, so they
>> sample
>>>> difference spaces. The energies you observe reflect that difference.
>>>>
>>>> Mark
>>>>
>>>> On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have a system containing of a virtual site of carbon connected
>>>>> symmetrically to two dummy massive sites (no charge). like :
>> M---C---M
>>>>> My problem is the results I get from simulation of this system is not
>>>> equal
>>>>> with results of single Carbon system simulation with mass of 2M (at
>>>> exactly
>>>>> similar conditions)?
>>>>> They produce different LJ coul energies, I have even tried for
>>>> non-charged
>>>>> systems.
>>>>>
>>>>> Thank you in advance for help,
>>>>> Best regards
>>>>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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