MBG wiki
|
RecentChanges
|
Blog
|
2024-04-20
|
2024-04-19
Editing Performing a molecular dynamics simulation in a hexagonal cell
Using an orthogonal cell for a periodic boundary simulation of a cylindrically-shaped molecule is one of the least efficient choices : the diagonal distances between neighboring images of the solute are much larger than those aimed for. The result is that a significant unit cell volume (and a few thousand water molecules) are being simulated needlessly. A hexagonal cell is a much better solution (make a drawing of the lattice to convince yourself): [[image: dna in hexagonal cell]] The difference in the number of waters needed for the simulation can be quite significant. With a border of 15 Angstroem and an orthogonal box NAMD reports (for the same solute) : <code> Info: **************************** Info: STRUCTURE SUMMARY: Info: 25117 ATOMS Info: 17038 BONDS Info: 9599 ANGLES Info: 2228 DIHEDRALS Info: 68 IMPROPERS Info: 0 EXCLUSIONS Info: 22 CONSTRAINTS Info: 176 FIXED ATOMS Info: 24569 RIGID BONDS Info: 0 RIGID BONDS BETWEEN FIXED ATOMS Info: 50254 DEGREES OF FREEDOM Info: 8647 HYDROGEN GROUPS Info: 108 HYDROGEN GROUPS WITH ALL ATOMS FIXED Info: TOTAL MASS = 154535 amu Info: TOTAL CHARGE = 8.23289e-07 e Info: ***************************** </code> If a hexagonal cell is used, the numbers are : <code> Info: **************************** Info: STRUCTURE SUMMARY: Info: 15436 ATOMS Info: 10588 BONDS Info: 6374 ANGLES Info: 2228 DIHEDRALS Info: 68 IMPROPERS Info: 0 EXCLUSIONS Info: 22 CONSTRAINTS Info: 176 FIXED ATOMS Info: 14894 RIGID BONDS Info: 0 RIGID BONDS BETWEEN FIXED ATOMS Info: 30886 DEGREES OF FREEDOM Info: 5416 HYDROGEN GROUPS Info: 108 HYDROGEN GROUPS WITH ALL ATOMS FIXED Info: TOTAL MASS = 96259.7 amu Info: TOTAL CHARGE = 8.23289e-07 e Info: ***************************** </code> Running a simulation with a hexagonal cell is not difficult but you will have to get a couple of sin()s and cos()s correct. The easy bit first [ and assuming that (i) you do a DNA run, and, (ii) you've already done the Dickerson tutorial ]. When using VMD's /solvate/ pluggin, instead of <code> ... # # Make water box # solvate psfgen_ions.psf psfgen_ions.pdb -o hydrated -b 1.80 -t 15.0 ... </code> give <code> ... # # Make water box # package require hexsolvate hexsolvate psfgen_ions.psf psfgen_ions.pdb -o hydrated -b 1.80 -t 15.0 ... </code> Now, the geometry exercise : with a hexagonal lattice the cell basis vectors are no longer orthonormal. You will have to determine them by hand and use your findings in the heating-up NAMD script. To aid your quest, here is an example : If the output from *pdbset* for your (hexagonal) box is : <code> Orthogonal Coordinate limits in output file: Minimum Maximum Centre Range On X : -37.70 36.28 -0.71 73.98 On Y : -29.17 29.17 0.00 58.34 On Z : -25.62 25.62 0.00 51.24 </code> then, the NAMD script should be given something like : <code> ... # # Particle Mesh Ewald parameters. # Pme on PmeGridsizeX 80 # <===== CHANGE ME PmeGridsizeY 56 # <===== CHANGE ME PmeGridsizeZ 56 # <===== CHANGE ME ... cellBasisVector1 73.98 00.00 00.00 # <===== CHANGE ME cellBasisVector2 00.00 43.75 25.26 # <===== CHANGE ME cellBasisVector3 00.00 00.00 51.24 # <===== CHANGE ME cellOrigin 0.00 0.00 0.00 # <===== CHANGE ME ... </code> Can you work out why ?
Summary:
This change is a minor edit.
Username:
Replace this text with a file.