Simulation - Simulate the soup

CAP - Catabolite gene Activating Protein (1BER)

Endonuclease PvuII bound to palindromic DNA recognition site CAGCTG (1PVI)

GCN4 - leucine zipper transcription factor bound to palindromic DNA recognition site ATGAC(G)TCAT (1YSA)

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Simulate the soup

°	Preparing a simulation - Define and fill the cell

First define a simulation cell with true walls or periodic boundaries, then fill it with objects and water . A more sophisticated way of filling the cell includes pKa prediction, counter ion placement and a simulation of the solvent to arrive at the right density .

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Boundary
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Set cell boundary

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Cell
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Set/get simulation cell dimensions

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FillCellObj
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Fill simulation cell with object

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FillCellWater
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Fill simulation cell with water

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Force fields - Get the recipe

Choose the force field and the force cutoff for non-bonded interactions, calculate electrostatic forces without a cutoff using PME for accurate results. In special cases, you may want to scale or exclude some force field components. The force field and AM1BCC atom types can also be retrieved to visualize YASARA's assignments.

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Cutoff
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Set force cutoff distance

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ForceField
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Set force field

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Force<Atom|Res|Mol|Obj|All>
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Set/get force on atoms

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Interactions
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Set force field terms

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Longrange
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Set long range interactions

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ScaleForce
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Set/get force scaling factors

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ShowSimGrid
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Show simulation grid

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SimSpeed
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Set simulation speed

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TypeAtom
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Get the atom type

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Simulation parameters - Choose your favorite ingredients

Switch between normal molecular dynamics at a given temperature, simulated annealing with a certain cooling level and energy minimization with a maximum step size . Control the pressure in the cell, set the simulation time, the time step and the number of screen updates per simulation step .

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AnnealSteps
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Set simulated annealing steps

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MinStep
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Set energy minimization step

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PressureCtrl
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Set pressure control

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SimSteps
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Set number of simulation steps per screen update

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Temp
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Set/get simulation temperature

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TempCtrl
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Set temperature control

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Time
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Set/get simulation time

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TimeStep
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Set simulation time step

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Restraints
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Enforce distances and dihedral angles

In addition to simply linking atoms with a spring , you can determine NMR structures using the same functions as XPLOR to restrain distances and dihedral angles individually or all together via a restraint file . The violation energies and statistics can be obtained using various potential functions and parameters like distance averaging . The restraints can be listed , selectively shown (satisfied restraints in green, violated ones in red), styled, hidden or deleted. Floating assignments can also be analyzed.

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AddSpring
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Link atoms with a spring

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DelRest<Obj|All>
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Delete restraints

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HideRest<Atom|Res|Mol|Obj|All>
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Hide restraints

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LoadTbl
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Load XPLOR distance and dihedral angle restraints

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ListFloat<Obj|All>

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List floating assignments

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ListRest<Atom|Res|Mol|Obj|All>
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List restraints and energies

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RestEnergy<Obj|All>
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Calculate restraint energies

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RestViol<Obj|All>

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Get restraint violation statistics

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RestrainDis
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Restrain distance

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RestrainDih
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Restrain dihedral angle

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RestrainPar
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Set/get restraining parameters

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RestrainPot
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Set/get restraining potential function

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SaveTbl
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Save XPLOR distance and dihedral angle restraints

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ScaleRest<Atom|Res|Mol|Obj|All>
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Scale restraints

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ShowRest<Atom|Res|Mol|Obj|All>
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Show restraints

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Running a simulation - Keep the soup from boiling

When everything is ready, start the simulation . Note the possibility to save and restore simulation snapshots in the File menu. When running a non-realistic simulation (like high temperature NMR structure generation or some modeling tasks), you can fix and free atoms or correct cis-peptide bonds and wrong isomeres on the fly, reporting these errors when needed.

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CorrectCis
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Correct cis-peptide bonds during simulation

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CorrectConv
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Correct naming conventions during simulation

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CorrectIso
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Correct wrong isomeres during simulation

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Fix<Atom|Res|Mol|Obj|All>
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Fix atoms during simulation

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Free<Atom|Res|Mol|Obj|All>
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Free atoms during simulation

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Sim
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Control simulation

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WarnIsError
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Treat warnings as errors