FillCellObj

The FillCellObj command fills the simulation cell with copies of the selected object. No additional objects are created, instead the copies become part of the original object.

The Copies and Density parameters allow you to request either a certain number of copies or a certain density, but not both at the same time. If a density is requested, YASARA will calculate the required number of copies according to the following formula (Density in [g/ml], Volumes in [A] and SolventMass in [g/mol]):

Contrary to FillCellWater , this command cannot make use of a predefined optimally packed example configuration and thus has to iteratively place the copies at random positions, trying to avoid bumps with the remaining atoms in the cell. BumpSum is the initially allowed sum of bumps, but will be increased automatically if needed to reach the requested number of copies. If too many bumps are present, it may become impossible to start a simulation. The solution is to start with a larger cell and then reduce its size during a simulation.

If you want to use FillCellObj to fill the simulation cell with a solvent other than water, follow these steps:

Load the solute.
Create the cell.
Build the solvent molecule (watch the help movie 'Building small molecules' for hints).
Use FillCellObj to fill the cell, specifying the actual experimentally measured solvent density.
Fix the solute.
Perform an energy minimization.
Set the pressure control to match your solvent residue name and solvent density.
Run a normal MD simulation until the solvent density displayed in the simulation HUD has reached the correct value.

Example 1:

Example 2:

Fill simulation cell with randomly placed copies of object methanol, allowing bumps up to 8 A and trying to reach a density of 0.7872 g/mol.

# EXAMPLE FillCellObj Vesicle # Requires YASARA Dynamics DelAll # Set test to 1 for a quick test, 0 for the real vesicle modeling test=1 # Radius of the lipid vesicle, measured at the boundary between outer and inner membrane radius=40. # Length of a lipid molecule lipidlen=25. # Area in A^2 occupied by a lipid molecule in the membrane (measured in its middle) lipidarea=53. # The composition of the membrane: an alternating list of percentages and corresponding # lipid names (.yob files). The percentages should sum up to 100. Here we use # 70% Phosphatidylcholine (dopc.yob) and 30% Phosphatidylserine (dops.yob) composition=70,'dopc',30,'dops' # Initial vesicle zoom factor, increase in case of a 'Search Grid Overflow' error message zoom=1.6 # No changes needed below this point types=count composition/2 # Calculate the number of lipids in inner(1) and outer(2) membrane for i=1 to 2 lipids(i)=0+sqr (radius+lipidlen*(-1.5+i))*Pi*4/lipidarea # Load single lipid molecules, the terminal carbons in # the two lipid tails must be named CM1 and CM2. for i=1 to types lip = LoadYOB (composition(i*2)) # Orient along the major (X-) axis NiceOriObj (lip) # Make sure the phosphate looks to the left side x=PosAtom Element P Obj (lip),CoordSys=global if x>0 RotateObj (lip),Y=180 # Freeze this orientation in the actual atom coordinates TransformObj (lip) # Speed up the graphics, the lipid vesicle will be large Style BallStick HideAtom Element H Antialias No LightSource Shadow=0 Console Off # Loop over inner and outer layer for i=1 to 2 # Now we want to equally distribute the lipids on a sphere # First get the next Fibonacci number after lipids(i) iqa=0 iqb=1 do iqc=iqa+iqb iqa=iqb iqb=iqc while iqb<lipids(i) r=(radius+lipidlen*(-1.5+i)) if not test r=r*zoom # Finally, loop over all required lipids j=0 for k=1 to iqb # Get coordinates of point j on the sphere, roughly equally distributed. # Mathematicians write papers about algorithms like this one.... ;-) ooiqb=1./iqb j=j+iqa if j>iqb j=j-iqb if rnd iqb<lipids(i) xb=ooiqb*k yb=ooiqb*j ph=yb*360 ct=(xb*-2+1) st=sqrt (1.-ct*ct)*r # posxyz are the 3D coordinates on the sphere surface posx=st*cos ph posy=st*sin ph posz=ct*r # Get a new lipid molecule, chosen randomly according to membrane composition percent=rnd 100 compsum=0. for l=1 to types compsum=compsum+composition(l*2-1) if compsum>percent break lip=DuplicateObj (l) # Orient the lipid normal to the sphere surface RotateObj (lip),Y=(-asin ct-180+i*180) RotateObj (lip),Z=(ph) # Move to the sphere surface MoveObj (lip),(posx),(posy),(posz+200) # Whenever we got 250 objects, join them together, # since YASARA's object limit is 250 if Objects==250 or k==iqb-1 JoinObj not 1-(types+i),(types+i) if k%25==0 ShowMessage 'Building layer (i), (k*100/iqb)% completed' Wait 1 RenameObj (types+1),Inner RenameObj (types+2),Outer DelObj not Inner Outer CenterObj all Console On # Build a single sodium ion in the middle, this will be the fixed anchor # for pulling the lipids together na=BuildAtom Na FixObj (na) PosObj all,0,0,200 if test # Just a test, cut the vesicle open for visualization DelRes globalX<0 globalY>0 globalZ<200 ColorAtom Element C with 2 bonds to Element C Obj Inner,Green ColorAtom CM1 CM2 Obj Inner,Green Ori Alpha=-16.751, Beta=340.746, Gamma=3.521 Antialias Yes LightSource Shadow=65 HideMessage else # Pull the lipids to their final position during a simulation # First remove bumps ShowMessage 'Removing bumps...' ForceField Amber99 Cell Auto Cutoff 5.24 TempCtrl SteepDes Sim On Wait SpeedMax<3000 # Now pull the lipids to the final distance ShowMessage 'Starting energy minimization to reach final distance...' AddSpring Element N Obj Inner,Element Na,Len=(radius-lipidlen+3),SFC=(350./radius) AddSpring CM? Obj Outer,Element Na,Len=(radius+3),SFC=(350./radius) TempCtrl Anneal # Wait until the energy minimization converged, then pull stronger do Wait 100 t=Temp while t>100 ScaleForce Bond,5.0 # This continues forever, if the temperature gets close to 0K, we are done

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Fill simulation cell with object

Example 1:

Example 2:

Example macro 1:

Example macro 2: