The MS.log and log4j files were unified into a single log file at some point in 10.1, I believe. Since then, 9MB has been the default log file size, and the logs will roll over automatically when they reach that size (they also automatically rollover at 12:00 AM every day). If you want to change the default file size, you can do that in the log4jMethodServer.properties file located in <Windchill>/codebase/WEB-INF. You can change the default by setting one of the below properties to the max size you want your log files to be:
log4j.appender.methodServerLogFile.MaximumFileSizeInBytes
log4j.appender.methodServerLogFile.MaximumFileSizeInMB