Use SSHFS to conveniently mount a remote file system on your local machine, all over ssh. You'll be able to perform any operation on the mounted files as if they were stored locally.
Once you've installed SSHFS (available on the Ubuntu repositories or through osxfuse on OS X) create a mount point (I've created a directory called tinis for this purpose):
mkdir -p ~/mnt/tinis
Now go ahead and mount your remote file system:
sshfs -o allow_other email@example.com:/ ~/mnt/tinis
The allow_other option allows non-rooted users have read/write access. You'll now find all of your remote files in ~/mnt/tinis. Copy files to ~/mnt/tinis and they'll be uploaded in the background. Once you're done, unmount using:
Your large simulations will be easier to manage (bonus: try monitoring ongoing simulations locally with gnuplot).