Okay well first off in order to run your own server with hamachi were going to need to download hamachi from this site: https://secure.logmein.com/products/.../download.aspx [Download Unmanaged one]
Next we are going to need to download the server files from the minecraft website: http://www.minecraft.net/download.jsp
or just download the files I am going to upload.
Pictures And instructions
1. We are going to need to start up hamachi and create our own network when you create your own network.
Its up to you what your passwords going to be but you need a network name something you can remember to let people into your server.
2. Next we are going to need to our server files. First off we are going to have to run the file minecraft server.jar the file I am going to be giving you in the uploaded attachment. Your going to want to create a new folder and naming it whatever you want but place your .jar file in that folder and run it. After a second or two your going to see a couple of files pop up in your folder because the .jar is going to need to create these files for our server.
3. Once we get our files we are going to go to the file named server properties. Now we don't have a program to open it automatically were going to open it with note pad.
4. With our file open with note pad were going to go back to hamachi while its still running and above our network you should see something that looks like a IP address were going to enter that for our servers IP address underlined in the picture below.
5. Now that we have our Servers IP set up were going to have to change one more thing for you to not get an error. Where it says online-mode=true in your notepad for your server your going to want to make it online-mode=false.
This is what I have to do but I used a cracked version so maybe you won't have to change it who knows. And your going to want to leave the port number as is. The rest you can change to your liking.
6. Starting your server up your going to have to run that .jar file I gave you earlier make sure its still in the folder and its going to load up your world and prepare everything for you.
7. Getting your friends to join your going to have to have them join your hamachi network and for the multi player IP its going to be your hamachi IP.
Once they join both your Hamachi network and enter you Hamachi IP they should be able to get on minecraft as long as you still have your server running from your .jar file.
If you have any questions referring on how to get your server running or what not feel free to ask me I would love to help.
Its helpful to have a high ram to run both minecraft and your server.
Virus Scans on server file.
minecraft_server.jar - Jotti's malware scan
VirusTotal - Free Online Virus, Malware and URL Scanner