parm protein.prmtop trajin md1.mdcrd trajin md2.mdcrd trajin md3.mdcrd trajin md4.mdcrd trajin md5.mdcrd trajin md6.mdcrd trajin md7.mdcrd trajin md8.mdcrd reference protein.inpcrd rms ToFirst :1-130&!@CA= first out rmsd_protein.agr mass