The simulation is a Coarse-Grained simulation, and I went through the following steps:
(1) Put position restraints (PR) on protein+lipid heads first (this is done in multiple steps, with position restraints on lipids and protein lifted slowly)
(2) Next, equilibration with protein backbone constrained.
(3) Lift the PR and do the production run.
There are two issues: (1) The initial configuration file generated using insane.py contained three water beads inside the protein. (2) Next, instead of the expulsion of water beads, they rush inside during the first equilibration step.
Please let me know if this is commonly observed, and if this is expected. If no, then what are the possible solutions?
Any kind of help is appreciated!!! Thank you :)
The answer to this depends on the specifics of your system. What do you meant by water went inside protein? Is it like a cavity that completely isolated from surrounding? Protein is a linear polymer and if you meant by 'inside' the interior of the protein tertiary structure, then it may be open so that water can get in.
Kolattukudy P. Santo Thank you for the quick reply! By cavity, I meant it should be isolated from the surrounding. There is no "cavity/hole/pore" due to tertiary structure arrangement. The water beads enter during the first two steps during equilibration and not during the production run (in fact, they start leaving, but there are some which get stuck). I was wondering if it is an artifact of the equilibration protocol, or not. I am attaching a figure for your reference. (green) water beads (rest) protein.
Riya Samanta : does water go inside protein when you solvate the system with water ? I mean after gmx solvate?
If yes, you can prevent it by changing the vanderwall radius of one or more protein CG atoms in the vdwradii.dat
Kolattukudy P. Santo Thank you so much!
I haven't used gmx solvate to solvate the system. In insane.py, it adds water beads to the system. However, in this case, insane.py adds three water beads "inside" the protein as well.
OK, let me try that out. But would that help if water beads enter during the equilibration? I mean, it seems as if they are entering the protein domain from the side too. Wouldn't it start affecting the intra-protein interactions?
Riya Samanta : Copy the vdwradii,dat file from the source directory to working directory. Change radius of C to 0.5 or larger in the vdwradii.dat , then do gmx solvate . This will exclude water beads from the neighborhood of hydrophobic protein beads (I guess C1, C2 ...). After solvating the system, you may change the radius back to the original value (or delete from working directory) . But I guess this particular source file is not used by mdrun, so it doesn;t matter.
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