When we perform MD simulation of a protein in a solvent box at constant temperature presssure condition then we generaly see that initially volume gets decreased and then fluctuate around a constant value.In my case protein and solvent box contain total around 3.5 lakh atoms and we perform 500 ps MD simulation at NPT condition using charmm forcefield and NAMD.The volume gets constantly decreasing upto that timescale.Probably as a consequence of this problem when we were trying to pull one end of that protein starting from one of the equilibrated structures using Steered Molecular Dynamics simulation the volume of the box decrease so rapidly that the simulation stops before unfolding the protein.
I am a bit confused, cause in the title you say that the volume does not reach a stable value during equilibration, but then in the message you say that you use the equilibrated structure to perform SMD. So, the system crashes after 500 ps of equilibration or production? For how long have you run your equilibration? Have you changed the values of PMEGridSize or CellBasisVector from the equilibration process to production?
I ran the NPT equilibration for 500 ps and upto that timescale volume didn't converge.Well one thing I forgot to mention.I ran that 500 ps NPT simulation applying some harmonic constraints to all the heavy atom and allowing all the hydrogen and solvents and ions to move freely.Then further I ran NPT simulation gradually relaxing that constraint and the final NPT run allow all the atoms present in the system to move freely.Then I performed NVT production run for 10 ns.Then I took one structure from that 10 ns NVT trajectory and performed SMD.Then during SMD system got crashed.I didn't tried with changing PMEGridSize but right now I am running that simulation with a little different CellBasisVector value.I am not sure whether this will improve the situation.
1) Using harmonic constraints to the protein during equilibration should not be related with a drastic change in the system's volume.
2) If the volume of your system was still decreasing at the end of equilibration, why did you move onto production? Certainly, you did not have an equilibrated system when starting your SMD simulation.
3) In my previous message I should have also asked if you are using the coor, vel and xsc files generated in the last step of your equilibration to start the production run. As you know, the volume of the system will fluctuate, slightly changing the dimensions of your simulation box. These values are stored in the xsc file, so it is wise to use them at the beginning of each consecutive run.
4) PMEGridSize values depend on the CellBasisVector ones, so you have to be careful when changing ones but not the others. Also, if you are using xsc files to restart your runs, NAMD will get the current dimensions of the box from there and not from the CellBasisVector. How did you obtain the CellBasisVector values for your first equilibration run? My guess is those values may not be accurate for your system, inducing the system to shrink and finally crash.
Initially I was using quite higher value of one of the cell basis vectors probably due to some mistake.Finally I entered right value of cell basis vector and now the volume gets converged. So , the problem was the wrong input of cell basis vector . I shall start SMD simulation and I hope this time system will not crash .Thank you very much Almudena Pino Angeles for your kind help .
That's great. I strongly suggest that you don't change those values anymore during the simulation and rely on the xsc files generated to keep up with the exact dimensions of the simulation box.
What is the origin of your protein structure? It is not uncommon to observe a modification in the system volume during equilibration, since the degree of the protein compactness in the crystallographic structure is different from what we should observe in solution. The important point is to wait for the system to equilibrate.
On equilibration: this is a much more complex discussion than usually considered. Each observed property will equilibrate in a different rate. And, for some of them, you will not observe equilibration in your trajectory in the currently accessible time scales. So the use of system descriptors as volume is a simple and initial strategy, but you need to move to additional strategies, such as the RMSD (more the stability than the magnitude of the value, if you do not see lost in secondary structure), secondary structure content, DSSP and radius of gyration.
Also, take a look at your SMD protocol and check if every parameter is as it should be, or if some of them could be related to the crash you reported.
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