From: Morgan, Brittany (Brittany.Morgan_at_umassmed.edu)
Date: Thu Mar 06 2014 - 12:26:02 CST
It sounds like you have other (small) molecules besides water and ions in your system. Did you equilibrate your water/solute mix by itself (in NVT) before adding the protein to see if the pressure is around 1 atm at that density and volume? Physically, depending on how crowded the environment is, your system might be experiencing high van der waals repulsion which can cause high pressure (in NVT) or force it to expand (in NPT). If you want to enforce a certain density, you may have to increase the pressure to match what it was initially.
From: Roy Fernando [roy.nandos_at_gmail.com]
Sent: Thursday, March 06, 2014 1:03 PM
To: Morgan, Brittany
Cc: Kenno Vanommeslaeghe; ivangreg_at_gmail.com; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: How to maintain Density constant?
Yes, I did. I can see that the system has expanded. But throughout the system it maintains a uniformity. I mean, the protein sits closer to the center of the box and then the water and other solutes move randomly. I transferred the protein to this system after equilibrating in water for 20ns. In this system protein seem to be increasing in size. This is again an indication of something unphysical going on, because in the new environment ( which is crowded ) I would expect the system to assume a more compact structure than trying to be more relaxed.
I am trying out all the possibilities here :).
On Thu, Mar 6, 2014 at 12:41 PM, Morgan, Brittany <Brittany.Morgan_at_umassmed.edu<mailto:Brittany.Morgan_at_umassmed.edu>> wrote:
Have you looked at your system visually after the density decreases? You would be able to tell, as Ivan suggested, if your system is diffusing because the periodic boundary conditions are not set correctly. Also, I'm assuming you have a 'typical' system of a protein in water box. Alternate solvents, membranes, etc. might have their own special issues.
From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] On Behalf Of Roy Fernando [roy.nandos_at_gmail.com<mailto:roy.nandos_at_gmail.com>]
Sent: Thursday, March 06, 2014 12:28 PM
To: Kenno Vanommeslaeghe; ivangreg_at_gmail.com<mailto:ivangreg_at_gmail.com>
Subject: Re: namd-l: How to maintain Density constant?
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.
On Thu, Mar 6, 2014 at 11:55 AM, Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu<mailto: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 Gregoretti, PhD
On Thu, Mar 6, 2014 at 10:57 AM, Kenno Vanommeslaeghe
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
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.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:12 CST