Welcome. This site is dedicated to newbie linux user help. Your honest appeal that you are posting this not as a user but for certain academic purpose deserves honest help too.
There are various bio-mathematical and molecular system simulators available that run over scientific linux. Click here for list and useful links.
. Also these are useful and free scientific-mathematical applications
to run over linux.
When your linux is running you may come back if you need help as a user.
I hope this helps.