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

[David]

On Wed, 2005-04-27 at 10:43 -0500, Zhiyong Zhang wrote:
> Dear gmx users,
> 
> For the same protein, I performed a MD simulation using Cut-off and PME,
> respectively. The following are parameters:
> 
You are using very different setup and give too little information.
How large is the protein?
Was there solvent in the simulations?
If so where is the solvent energy?


> 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/
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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