Introduction Force Field Assembly The Calculate module offers three customized molecular mechanics functions: Minimize for Energy Minimization, Dynamics for Molecular Dynamics and Anneal for Simulated Annealing. These functions are the results of several years experience with the rrDNAv1 model. Many decisions have been made for you and as a result you can use these functions with minimal input. There are limitations. These functions can only operate on an entire model. The methods that these functions are based upon can operate on a selected part of a model. The Dynamics and Anneal functions can only be applied to circular rrDNAv1 models. Minimize This function carries out an energy minimization calculation. It will use the PR+ Conjugate Gradient method (CGPR) and if the line search fails (which is not a fatal error), a small number of steps of the Simple Steepest Descent (SimpleSD) method are applied as a correction. Usually, the correction makes no difference to the outcome; this would indicate that there are no further opportunities to lower the energy. One would have to get out of this local minimum and explore other minima. This function makes the following settings: Attribute Value MolMech.UpdateInterval 25 The arguments are: Keyword Description Default Value dnamodel Target for minimization: a Model object for a rrDNAv1 model - numsteps Maximum number of CGPR steps 5000 printdiv Number of print divisions or if negative the interval between prints (MolMech.NumberOfPrintDivisions) 5 Customized Molecular Dynamics The remaining two functions make use of a class derived from the Motors class for molecular dynamics. This class overrides the userafter method and makes the following settings: Attribute Value UpdateInterval (MolMech) 25 StepSize (Motors) [picoseconds] 0.025 ThermalizationInterval (Motors) 100 UserBeforeInterval (Motors) 0 UserAfterInterval (Motors) 10000 When the class is initialized, up to two attempts to calculate the linking number are made. If the first attempt fails, the structure is minimized before the second attempt. If the second attempt also fails, the class cannot be initialized. The linking number calculation fails when there is no evidence that the model contains two circles. If the structure cannot be repaired by a short minimization, to the extent that a linking number calculation can proceed, then it is quite clear that the model is defective and a molecular dynamics calculation is unlikely to succeed. The linking number is stored. At every UserAfterInterval steps of the molecular dynamics simulation, the userafter method calculates the linking number and compares it with the stored value. If the numbers are different, this would indicate that strand crossing has occurred and the simulation is stopped immediately (by raising a Runtime exception). Dynamics This function makes use of the customized molecular dynamics class to carry out a molecular dynamics simulation. The arguments are: Keyword Description Default Value dnamodel Target for molecular dynamics: a Model object for a rrDNAv1 model - picosec Duration of the simulation in picoseconds - startT If not None, set the temperature to this value before the simulation None finalT If not None and thermdiv is greater than 0, adjust the temperature at every thermdiv step, such that the temperature is at this value at the end of the simulation. This is only a target and the final temperature may not be exactly this value. None therm Thermalization method: other acceptable values are "SCALE" and "BERENDSEN". "NEW" thermdiv Thermalization Interval (Motors.ThermalizationInterval) 100 Note that "-" indicates that there is no default value (and a value must be supplied) and "None" is an actual value. Set thermdiv to 0 for a free dynamics simulation; settings for therm and finalT will have no effect. Anneal This function makes use of the customized molecular dynamics class to carry out a simulated annealing calculation. The arguments are: Keyword Description Default Value dnamodel Target for simulated annealing: a Model object for a rrDNAv1 model - highT Highest temperature [K] 500 heat First, the model is heated from 1 K to the highest temperature over this duration [picoseconds] None hold Then, the model is held at the highest temperature for this length of time [picoseconds] None cool Finally, the model is cooled to 1 K over this period [picoseconds] None Note that "-" indicates that there is no default value (and a value must be supplied) and "None" is an actual value. The thermalization method used for heating is "NEW" and "SCALE" is used for the remaining stages. If any duration (heat, hold, cool) is at the default value, it is calculated as multiples of one quarter of the total atom count for the model, rounded to the nearest hundred. The multipliers are 1, 1 and 10 respectively. For example, in a 3DNA model of 1236 basepairs, there are a total of 3708 atoms. A quarter of that is 927 and the nearest hundred is 900. Thus heat and hold will be 900 ps and cool will be 9000 ps, unless the user supplies actual numbers. Analysis Service Functions