can anyone please tell me, if i select 42 then wheather it will calculate the protein-protein interaction energy? because i did not define two proteins in the mdp file.i just mentioned protein.I am not understanding this. thanking you
On 1/8/19, SHAHEE ISLAM <islamsha...@gmail.com> wrote: > hi, > i want to calculate interaction energy between two protein. > In my system there are two proteins,waters and ions.In my .mdp file > the, energygrps = PROTEIN W ION > i am using this command > gmx energy -f ../dynamic.edr -s ../eq.gro -o ener.xvg > then the following options are coming > > 1 Bond 2 G96Angle 3 Proper-Dih. 4 > Improper-Dih. > 5 LJ-(SR) 6 Coulomb-(SR) 7 Potential 8 > Kinetic-En. > 9 Total-Energy 10 Temperature 11 Pressure 12 > Constr.-rmsd > 13 Box-X 14 Box-Y 15 Box-Z 16 Volume > 17 Density 18 pV 19 Enthalpy 20 Vir-XX > 21 Vir-XY 22 Vir-XZ 23 Vir-YX 24 Vir-YY > 25 Vir-YZ 26 Vir-ZX 27 Vir-ZY 28 Vir-ZZ > 29 Pres-XX 30 Pres-XY 31 Pres-XZ 32 Pres-YX > 33 Pres-YY 34 Pres-YZ 35 Pres-ZX 36 Pres-ZY > 37 Pres-ZZ 38 #Surf*SurfTen 39 Box-Vel-XX 40 Box-Vel-YY > 41 Box-Vel-ZZ 42 Coul-SR:Protein-Protein > 43 LJ-SR:Protein-Protein 44 Coul-SR:Protein-W > 45 LJ-SR:Protein-W 46 Coul-SR:Protein-ION > 47 LJ-SR:Protein-ION 48 Coul-SR:W-W > 49 LJ-SR:W-W 50 Coul-SR:W-ION > 51 LJ-SR:W-ION 52 Coul-SR:ION-ION > 53 LJ-SR:ION-ION 54 T-Protein 55 T-W 56 T-ION > 57 Lamb-Protein 58 Lamb-W 59 Lamb-ION > > if i select 42 and 43. will it give me the total energy value > considering both proteins. > or what should i correctly select. > thanking you > Shahee Islam > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
