[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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