[gmx-users] Different coulomb energies of protein by Cut-off and PME
Zhiyong Zhang
Zhiyong.Zhang at uth.tmc.edu
Wed Apr 27 17:43:33 CEST 2005
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/
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