[gmx-users] Different coulomb energies of protein by Cut-off and PME
Zhiyong Zhang
Zhiyong.Zhang at uth.tmc.edu
Thu Apr 28 17:49:14 CEST 2005
Hi,
Thanks for your reply!
The protein has 51 residues and 530 atoms. I included explicit waters in
the simulations. The following are coulomb energies of the total system
from Cut-off and PME, respectively.
Cut-off:
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Coulomb-14 5793.36 39.3909 39.1433 -0.00305485
-15.2743
Coulomb (SR) -248203 671.972 668.068 -0.050111
-250.555
Coulomb (LR) -3725.48 425.932 418.264 0.0557401
278.701
Total -246136 -- -- --
--
PME:
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Coulomb-14 5800.09 42.6203 42.4826 -0.00197631
-11.8579
Coulomb (SR) -215201 573.112 573.087 -0.00309615
-18.5769
Coulomb (LR) -34776.9 45.6159 45.6125 0.00032001
1.92006
Total -244178 -- -- --
--
If you need any other information, please let me know. I noticed that,
the coulomb energies of the whole system are similar, why it is
different when I only considered protein?
Regards
Zhiyong
On Thu, 2005-04-28 at 01:27, David wrote:
> 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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