RcutLow 1.0to reject any move that puts any atom closer than 1 A distance from other molecules. This would also help to increase the code performance by avoiding reciprocal energy calculation. It would also prevent atom collapse for naked charge atom (no LJ interaction, e.g. hydrogens).
IntraSwapFreq 0.0. In addition, since ibuprofen is relatively large compare to void area in your system, it would more beneficial to use more swap moves.
CBMC_First 16and decreasing the CBMC trials for secondary atoms
CBMC_Nth 5. You could potentially do a benchmark to see which set of parameter would give you higher acceptance, or efficiency (accepted/CPU-time). Unfortunately the CBMC parameters is unique for each system, but you will get the general rule of thumb after few trials.
vmd OUTPUT_merged.psb OUTPUT_BOX_0.pdb
pbc box -color 4
pbc wrap -sel "resname PEVQ"
pbc wrap -sel "resname PEVQ" -all
pbc wrap -all
VDWGeometricSigma true. In addition, you might need to use
Exclude 1-3to consider 1-4 and 1-n interaction in sampling geometric of your molecule.
@Tom-Pope I looked at your system, and I believe the problem is in the parameter file.
This problem only happens when you are trying to construct a branching point that forms a plane and this a due to mathematical limitation.
Let's focus on the oxygen atom attached to the benzene ring in aspirin molecule. In your parameter file we have:
Angles parameter: Atom Types Ktheta(K) theta0(degree) OR CB CB 35056.0000 120.0000 CB CB CB 24227.6600 119.9770
We have one OR-CB-CB and two CB-CB-CB angles at this branching point.
Having 3 angles with equilibrium value near 120, it means they must be in the same plane. When you have flexible angles, if you pick an angle above 120 (let's say OR-CB-CB angle is 122), it means that sum of the both CB-CB-CB angles must be less than 238, otherwise you cannot construct such a geometry. If in your trial angle generation, you try angles with summation above 238, you will get this error message.
To solve your problem, I would suggest to fix the angles for OR-CB-CB, CB-CB-CB, CB-CB-HCMM. Its very important to make sure when you build your molecule, the CB-CB-CB, CB-CB-HCMM angles are exactly 120. Otherwise we would get the same error. Until we find another way around to solve this problem.
also I there is another error being generated in my Ibuprofen simulations: 'Wrapping molecules inside the simulation box 1:
Error: Multiple atoms with zero coordinates were found'
Please check you PDB file for simulation box 1. Sometimes packing or PSF generation failed which results in generating zero value for X, Y, and Z coordinates. If you found multiple molecules with zero coordinate, it means PSF generation failed due to possible mistake in topology file. You can look into the warning generated from vmd.