I'm going to confirm the protein-protein interaction energy. If I carry out MD simulations with
coulombtype = Generalized-Reaction-Field energygrps = Protein OTHER Then g_energy outputs 1= Bond 2= Angle 3= Proper Dih. 4=Ryckaert-Bell. 5= LJ-14 6= Coulomb-14 7= LJ (SR) 8= Coulomb (SR) 9= RF excl. 10= Potential 11= Kinetic En. 12= Total Energy 13= Temperature 14=Pressure (bar) 15= Box-X 16= Box-Y 17= Box-Z 18= Volume 19= Density (SI) 20= pV 21= Vir-XX 22= Vir-XY 23= Vir-XZ 24= Vir-YX 25= Vir-YY 26= Vir-YZ 27= Vir-ZX 28= Vir-ZY 29= Vir-ZZ 30= Pres-XX (bar) 31= Pres-XY (bar) 32= Pres-XZ (bar) 33= Pres-YX (bar) 34= Pres-YY (bar) 35= Pres-YZ (bar) 36= Pres-ZX (bar) 37= Pres-ZY (bar) 38= Pres-ZZ (bar) 39= #Surf*SurfTen 40= Pcoupl-Mu-XX 41= Pcoupl-Mu-YY 42= Pcoupl-Mu-ZZ 43= Mu-X 44= Mu-Y 45= Mu-Z 46=Coul-SR:Protein-Protein 47=LJ-SR:Protein-Protein 48=Coul-14:Protein-Protein 49=LJ-14:Protein-Protein 50=Coul-SR:Protein-Other 51=LJ-SR:Protein-Other 52=Coul-14:Protein-Other 53=LJ-14:Protein-Other 54=Coul-SR:Other-Other 55=LJ-SR:Other-Other 56=Coul-14:Other-Other 57=LJ-14:Other-Other 58= T-Protein 59= T-Other 60= Lamb-Protein 61= Lamb-Other I think numbers corresponding to protein-protein interaction energy are 9 46 47 48 49. Especially, I'm interested in dealing with 9, 'RF excl.'. Perhaps, this term means Reaction-field exclusion correction coded by Berk Hess, (http://www.gromacs.org/features/changes33.html) and affects 48, 'Coul-14:Protein-Protein'. Is it correct? Thanks. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
