[gmx-users] Calculate heat capacity

[maryam haji]

Dear gromacs users

My system contains protein(15 residue) and CNT and water molecules and ion.

at the end of .top file is
[ molecules ]
; Compound        #mols
Protein_chain_A     1
CNT                 1
SOL              6531
NA                  2

I want to calculate the heat capacity in ensemble NVT.outputs g_energy are:

-------------------------------------------------------------------
  1  G96Angle         2  U-B              3  Proper-Dih.      4
 Fourier-Dih.
  5  Improper-Dih.    6  CMAP-Dih.        7  LJ-14            8  Coulomb-14

  9  LJ-(SR)         10  Coulomb-(SR)    11  Coul.-recip.    12
 Position-Rest.
 13  Potential       14  Kinetic-En.     15  Total-Energy    16
 Conserved-En.
 17  Temperature     18  Pressure        19  Constr.-rmsd    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  Coul-SR:Protein-Protein             40  LJ-SR:Protein-Protein

 41  Coul-14:Protein-Protein             42  LJ-14:Protein-Protein

 43  Coul-SR:Protein-CNT                 44  LJ-SR:Protein-CNT

 45  Coul-14:Protein-CNT                 46  LJ-14:Protein-CNT

 47  Coul-SR:Protein-SOL                 48  LJ-SR:Protein-SOL

 49  Coul-14:Protein-SOL                 50  LJ-14:Protein-SOL

 51  Coul-SR:Protein-NA                  52  LJ-SR:Protein-NA

 53  Coul-14:Protein-NA                  54  LJ-14:Protein-NA

 55  Coul-SR:CNT-CNT                     56  LJ-SR:CNT-CNT

 57  Coul-14:CNT-CNT                     58  LJ-14:CNT-CNT

 59  Coul-SR:CNT-SOL                     60  LJ-SR:CNT-SOL

 61  Coul-14:CNT-SOL                     62  LJ-14:CNT-SOL

 63  Coul-SR:CNT-NA  64  LJ-SR:CNT-NA    65  Coul-14:CNT-NA  66
 LJ-14:CNT-NA
 67  Coul-SR:SOL-SOL                     68  LJ-SR:SOL-SOL

 69  Coul-14:SOL-SOL                     70  LJ-14:SOL-SOL

 71  Coul-SR:SOL-NA  72  LJ-SR:SOL-NA    73  Coul-14:SOL-NA  74
 LJ-14:SOL-NA
 75  Coul-SR:NA-NA   76  LJ-SR:NA-NA     77  Coul-14:NA-NA   78
 LJ-14:NA-NA
 79  T-Protein_CNT                       80  T-Water_Ion

 81  Lamb-Protein_CNT                    82  Lamb-Water_Ion


when i select 15&17 i have a warning that include:

WARNING: nmol = 1, this may not be what you want.

i konw that nmol is the number of molecules.i have two question

1-how can i calculate nmol?

2-Is nmol=mol water+mol cnt+mol protein?

Thanks in advance