[gmx-users] Different coulomb energies of protein by Cut-off and PME
David
spoel at xray.bmc.uu.se
Thu Apr 28 19:57:14 CEST 2005
On Thu, 2005-04-28 at 10:49 -0500, Zhiyong Zhang wrote:
> 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?
Because protein-protein energy is implicitly contained in the PME
energy. See list archive for splitting the energy in groups.
>
> 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/
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list