[gmx-users] calculate interaction energy between two proteins
SHAHEE ISLAM
islamshahee at gmail.com
Tue Jan 8 12:29:42 CET 2019
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
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