[gmx-users] Different coulomb energies of protein by Cut-off and PME

[Zhiyong Zhang]

Dear gmx users,

For the same protein, I performed a MD simulation using Cut-off and PME,
respectively. The following are parameters:

For Cut-off:

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 5
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or no =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.0
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 1.4
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = Cut-off
; cut-off lengths        =
rvdw-switch              = 0
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

For PME:

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 5
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or no =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 0.9
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = Cut-off
; cut-off lengths        =
rvdw-switch              = 0
rvdw                     = 1.4
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

After simulations, I calculated the coulomb energies in the protein.

Cut-off:

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:Protein-Protein     -8733.4    314.267    287.225 -0.0883592  
-441.796
Coul-LR:Protein-Protein   -0.280069    254.458    250.858  0.0295494   
147.747
Coul-14:Protein-Protein     5793.36    39.3909    39.1433 -0.00305485  
-15.2743
Total                      -2940.32         --         --     --        
--

PME:

Energy                      Average       RMSD     Fluct.      Drift 
Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:Protein-Protein    -1314.89    79.1684    75.3171 -0.0140827  
-84.4963
Coul-LR:Protein-Protein         0          0          0       0         
0
Coul-14:Protein-Protein     5800.09    42.6203    42.4826 -0.00197631  
-11.8579
Total                        4485.2         --         --     --        
--

I noticed that, the total coulomb energies in the protein by Cut-off and
PME are quite different. Would you please explain it? Thanks!

Best wishes
Zhiyong Zhang
-- 
Postdoctoral Fellow,
School of Health Information Sciences,
University of Texas Health Science Center - Houston,
7000 Fannin St., suite 1480,
Houston, TX 77030, U.S.A.
email: Zhiyong.Zhang at uth.tmc.edu
http://www.biomachina.org/people/zhang/