After fresh installation:
yum update
Install CUDA toolkit and Nvidia driver
yum install kernel-devel kernel-headers gcc dkms acpid
echo "blacklist nouveau" >> /etc/modprobe.d/blacklist.conf
Edit /etc/sysconfig/grub
Append ‘rd.driver.blacklist=nouveau’ to end of ‘GRUB_CMDLINE_LINUX=”…”‘
grub2-mkconfig -o /boot/grub2/grub.cfg
mv /boot/initramfs-$(uname -r).img /boot/initramfs-$(uname -r)-nouveau.img
dracut /boot/initramfs-$(uname -r).img $(uname -r)
systemctl set-default multi-user.target
reboot
./cuda_7.5.18_linux.run
systemctl set-default graphical.target
reboot
Install Amber
see here for amber installation
Install VMD
Install precompiled version
./configure
cd src
sudo make install
Install from source code
....
Install CHARMM
see here