From: Roy Fernando (roy.nandos_at_gmail.com)
Date: Thu Mar 06 2014 - 11:28:23 CST
Hi Kenno, Ivan,
Thanks for detailed explanations.
While I understand the fundamental physics part, what I was looking for is
some insights about why my system displaying unphysical (or far from being
physical) behaviors.
I am not simulating a gas, I am simulating a protein in a solution. This
type of a system evolve under atmospheric pressure and therefore choosing a
NPT simulation makes sense to me. When an NPT simulation is chosen I am
allowing the system volume to fluctuate to maintain the pressure around
1atm. However, what I noticed was not a fluctuation. The density of the
system dropped by 40% because the system dimensions has increased by 20%. I
was trying to see if there are other processes that can be applied such as
maintaining some ion concentration (this system is neutral to balance the
charges). The density of the solution is expected to be around 1.1 g/cm^3
but I observed it to be around 0.6 g/cm^3
Thanks for your help.
Roy
On Thu, Mar 6, 2014 at 11:55 AM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:
> It's perfectly normal (and indeed unavoidable) in constant pressure
> simulations for the volume (and hence density) to equilibrate a bit, then
> fluctuate. As long as the change is not catastrophic (which was not
> indicated in Roy's e-mail), there's nothing to worry about. If the density
> is really important, one can run NVT, but then one has to give up control
> over the pressure.
>
>
>
> On 03/06/2014 11:34 AM, Ivan Gregoretti wrote:
>
>> Thank you Kenno.
>>
>> So, going back to try to help Roy.
>>
>> 1) Running MD simulations where you control both pressure and
>> temperature is routine. Kenno tells us that it makes no sense to also
>> try to impose a control on the volume. (Of course.)
>>
>> 2) Why is your system's density dropping? I wonder if the periodic
>> boundary conditions are properly set. I can picture a situation where
>> there is no boundary conditions and the molecules start to slowly
>> diffuse away from the center of mass of your system.
>>
>> Ivan
>>
>>
>> Ivan Gregoretti, PhD
>> Bioinformatics
>>
>>
>>
>> On Thu, Mar 6, 2014 at 10:57 AM, Kenno Vanommeslaeghe
>> <kvanomme_at_rx.umaryland.edu> wrote:
>>
>>> On 03/06/2014 08:23 AM, Ivan Gregoretti wrote:
>>>
>>>>
>>>> p V = n R T
>>>>
>>>> with n being the number of molecules and V being volume. It's an ideal
>>>> gas state equation. Notice that n/V is your density.
>>>>
>>>> In your molecular dynamics, n does not change, so, if you want to keep
>>>> the density constant, you need to run your simulation at constant
>>>> volume.
>>>>
>>>> Do I get it right Kenno?
>>>>
>>>
>>>
>>> Mostly. We usually don't simulate gases, so the ideal gas law you
>>> brought up
>>> is of very limited value, but there exist similar equations for liquids
>>> and
>>> solid, and one thing they all have in common is that (assuming n is
>>> constant) out of p, V and T (and also E and/or Q), you can set two to an
>>> arbitrary value, but then you don't have control over the other one(s);
>>> this
>>> is very fundamental and doesn't take advanced statistical mechanics to
>>> see.
>>> There exist mechanisms in nature to impose *some* combinations of these
>>> variables on a system, and these combinations ("ensembles" in
>>> thermodynamic
>>> speak) are often implemented in MD engines. The "constant pressure and
>>> volume" Roy asked for is not one of them; even if someone would somehow
>>> implement it, it would be of no practical relevance. Besides, the
>>> temperature would shift and fluctuate uncontrollably (remember, you can
>>> only
>>> choose 2), which is probably not what Roy (or anyone else) wants.
>>>
>>>
>
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