You can edit the myeclipse.ini file (open as text file) located in the MyEclipse installation directory and increase the -Xmx value to assign more memory depending on your workspace size and your applications usage.
For instance, the following settings may be preferable to the defaults.
If you are still seeing problems, then please share with us the below details to help us investigate further:
1. The MyEclipse version details from Help > About MyEclipse section.
2. The current value of -Xmx
3. Your workspace size approximately in MB/GB.
4. Workspace log file located at workspace dir/.metadata/.log