[gmx-users] Calculate heat capacity

[David van der Spoel]

On 2014-04-07 09:26, maryam haji wrote:
> Dear gromacs users
>
> My system contains protein(15 residue) and CNT and water molecules and ion.
>

If you want to compute the heat capacity of a complex system like that 
you have to perform simulations of exactly the same system at different 
temperatures and then extract cP = Delta E/ Delta T (or do a linear 
regression analysis). See Alexandra Patriksson and David van der Spoel: 
A temperature calculator for replica exchange molecular dynamics 
simulations Phys. Chem. Chem. Phys. 10 pp. 2073-2077 (2008)

> 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
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se