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I made a simulation of AQY1.By analizing volume with convex Hull from XTC ,i have noted an increase in volume during NPT simulation while It Is constant in NVT.By analizing RMSD It Is low so probably no conformational change.Why has this happend?
NVT means that the volume is constant. NPT means that the pressure is kept constant by changing the volume.
Yess but in NVT volume kept constant Is the One of the box i think or constant volume box has Also an impact on protein volume?
I don’t understand what you mean. Keeping the box volume constant may, or may not, affect the protein volume.
That’s the image of the volume of my protein along time.First 3000 ps are in NPT the second 3000ps in NVT.During the first 3000 ps my protein volume seems to increase but calculating RMSD it is not so high.Why this happend?
First, it is uncommon to run NVT after NPT. Is there a specific reason why you are doing that?
From the plot it’s very difficult to say why the volume of the protein is increasing. If the volume of the whole system increases (due to the barostat) it’s natural that the volume of the protein increases as well. You can see if the volume increase of the protein follows the volume change of the system by plotting them both at the same time.
Apart from that, my spontaneous thought is that it might be due to normal equilibration of the system. Do you see any volume change of the protein if you start with NVT?
Also, keep in mind that the change that you see is not very large. It’s approximately 3%. Is there are reason why are worried about that?
A specific requirements of my work is to run the in that order.I’m a newby in Molecular Dynamics so i don’t know if this change in volume is significant or not.I have seen that volume of simulation in NPT oscillates but doesn’t tend to increase.I have also supposed a possible protein conformational change but analizing RMSD it is quite low stable and similar beetween NPT and NVT.
When the system is in equilibrium the system volume fluctuates in an NPT ensemble. Usually, the system volume can change very quickly in the beginning (first 10 ps) of an NPT equilibration.
However, your change is later and smoother, so I just think it’s part of the equilibration process. Even if the specific requirements of your work is to do NPT followed by NVT equilibration, I think it would be interesting for you to monitor the protein’s change in volume if you do it the other way around. In that case, I would also recommend extending the runs slightly, since the change in volume is happening in the last third of the NPT equilibration. Due to the random nature of MD simulations, such a change could happen sooner or later than that if you repeat the simulation.
I also don’t know how you calculate the volume of your protein. Would an increased mobility of a few surface residues affect the calculated protein volume? In that case, that would not lead to a large RMSD of a protein.
i’m using convex hull function to calculate volume. Visually inspecting simulation it doesn’t seem to me that particular conformational changes happend.
With a 3% increase in volume (~1% in each dimension) I guess it would be difficult to see large changes.
i have calculated also volume using sasa function of GROMACS with sasa -tv the volume is constant in both ensamble by using sasa.Can this behaviour of volume be linked to convex hull function?
I’m not sure, but convex hull volume is a rough estimate and uses the outermost points (atoms). So, if they move a little further outwards it might have a noticeable (perhaps still not large) effect on the calculated volume.