[gmx-users] Charge grps and cut-off
Justin A. Lemkul
jalemkul at vt.edu
Sat Jul 17 13:41:13 CEST 2010
Sai Pooja wrote:
> Thanks Justin. How about note 3?
>
> The largest charge group contains 12 atoms.
> Since atoms only see each other when the centers of geometry of the charge
> groups they belong to are within the cut-off distance, too large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should consist of a few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>
> This note reappears no matter what the parameter file has. Does this
> mean I need to make changes in my top file or define charge groups?
>
Yes, something is wrong with the topology. You have a charge group that is
likely unacceptably large.
-Justin
> Pooja
>
>
> On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Sai Pooja wrote:
>
> Hi,
>
> This is the .mdp file that produces notes-3 and 4. However, the
> previous md file produces note-3.
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> dt = 0.002
> nsteps = 5000000
>
> ; OUTPUT CONTROL OPTIONS
> nstxout = 0 ; No output,
> except for last frame (coordinates)
> nstvout = 0 ; No output,
> except for last frame (velocities)
> nstfout = 0 ; No output,
> except for last frame (forces)
> nstlog = 500000 ; Write every
> step to the log
> nstenergy = 500000 ; Write
> energies at every step
> xtc_grps = Protein
> nstxtcout = 500000 ; Do not
> write a compressed trajectory
> energygrps = Protein Non-Protein ; Write energy
> information separately for these groups
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist = 5
> ns-type = Grid
> pbc = xyz
> rlist = 2.0
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype = Reaction-field-zero
> rcoulomb = 1.8
> epsilon_rf = 0
> vdw-type = Switch
> rvdw = 2.0
> rvdw-switch = 1.6
>
>
> Well, here's the problem. Read about proper usage of the switch
> function, especially the note about the size of rlist:
>
> http://manual.gromacs.org/current/online/mdp_opt.html#vdw
>
> -Justin
>
> ; Spacing for the PME/PPPM FFT
> 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
> epsilon_surface = 0
> optimize_fft = no
> ; Temperature coupling
> tcoupl = nose-hoover
> tc-grps = Protein Non-Protein
> tau_t = 0.2 0.2
> ref_t = 300 300
>
> ; Pressure coupling pcoupl = no
>
> ; OPTIONS FOR BONDS constraints = all-bonds
> constraint-algorithm = SHAKE
> shake_tol = 0.0001
>
> Pooja
>
>
>
> On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Sai Pooja wrote:
>
> Hi,
>
> I am trying to reproduce results from a paper which uses this
> cutoff. The work is on loop-folding and they use implicit
> solvent. I am using explicit solvent with charmm 27.
> Below is my
> mdp file. I am not sure if there is any advantage in using a
> large cut-off.
>
>
>
> Large cutoffs can cause artifacts. This .mdp file also does not
> match the error message you quoted before. If it is indeed
> accurate, then it looks like your .mdp file is being interpreted
> incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a
> misinterpretation, file a bugzilla. If you've simply posted the
> wrong file, please post the correct file, if necessary. But I'd
> suggest you do some homework about the effects of long cutoffs,
> especially if they deviate from what the force field derivation
> requires.
>
> -Justin
>
> ; VARIOUS PREPROCESSING OPTIONS
> title = NVT simulation (constant number,
> pressure and temperature)
> cpp = /lib/cpp
> define =-DPOSRES
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> dt = 0.002
> nsteps = 100000
>
> ; OUTPUT CONTROL OPTIONS
> nstxout = 10000
> nstvout = 0
> nstfout = 0
> nstlog = 10000
> nstenergy = 10000
> nstxtcout = 0
> xtc_precision = 0
> xtc-grps = System
> energygrps = Protein Non-Protein
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist = 5
> ns-type = Grid
> pbc = xyz
> rlist = 1.8
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype = PME
> fourierspacing = 0.12
> rcoulomb = 1.8
> epsilon_rf = 78
> vdw-type = Cut-off
> rvdw = 1.8
>
> ; 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
> epsilon_surface = 0
> optimize_fft = no
>
> ; Temperature coupling Tcoupl = Berendsen
> tc-grps = Protein Non-Protein
> tau_t = 0.2 0.2
> ref_t = 300 300
>
> ; Pressure coupling Pcoupl = Berendsen
> Pcoupltype = Isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = no ; Assign velocities to
> particles by taking them randomly from a Maxwell distribution
> gen_temp = 300.0 ; Temperature to generate
> corresponding Maxwell distribution
> gen_seed = 9999 ; Seed for (semi) random
> number generation.
>
>
> ; OPTIONS constraints = all-bonds
>
> Pooja
>
>
>
>
>
>
>
> On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
>
>
>
> Sai Pooja wrote:
>
> Hi,
>
> I am getting these notes when I run grompp:
>
> NOTE 3 [file Init/ffsb_init.top]:
> The largest charge group contains 12 atoms.
> Since atoms only see each other when the centers of
> geometry of
> the charge
> groups they belong to are within the cut-off
> distance, too
> large charge
> groups can lead to serious cut-off artifacts.
> For efficiency and accuracy, charge group should
> consist
> of a
> few atoms.
> For all-atom force fields use: CH3, CH2, CH, NH2, NH,
> OH, CO2,
> CO, etc.
>
> initialising group options...
> processing index file...
> Analysing residue names:
> There are: 3484 OTHER residues
> There are: 67 PROTEIN residues
> There are: 0 DNA residues
> There are: 0 RNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for Acceleration
> containing 11343
> elements
> Making dummy/rest group for Freeze containing
> 11343 elements
> Making dummy/rest group for VCM containing 11343
> elements
> Number of degrees of freedom in T-Coupling group
> Protein
> is 1777.76
> Number of degrees of freedom in T-Coupling group
> non-Protein is
> 20898.23
> Making dummy/rest group for User1 containing 11343
> elements
> Making dummy/rest group for User2 containing 11343
> elements
> Making dummy/rest group for XTC containing 10450
> elements
> Making dummy/rest group for Or. Res. Fit
> containing 11343
> elements
> Making dummy/rest group for QMMM containing 11343
> elements
> T-Coupling has 2 element(s): Protein non-Protein
> Energy Mon. has 2 element(s): Protein non-Protein
> Acceleration has 1 element(s): rest
> Freeze has 1 element(s): rest
> User1 has 1 element(s): rest
> User2 has 1 element(s): rest
> VCM has 1 element(s): rest
> XTC has 2 element(s): Protein rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge
> groups...
> Largest charge group radii for Van der Waals:
> 0.288, 0.263 nm
> Largest charge group radii for Coulomb:
> 0.288, 0.263 nm
>
> NOTE 4 [file nvtp.mdp]:
> The sum of the two largest charge group radii
> (0.551009) is
> larger than
> rlist (2.000000) - rvdw (2.000000)
>
> Can someone tell me how to correct these?
>
>
> Note 3 is explained in detail in the error message.
> Beyond that,
> read about the group concept in the manual.
>
> I've never seen Note 4 before, but a 2-nm cutoff is a
> bit strange
> for a protein simulation. Any reason you're using
> such large
> cutoffs? You may also want to provide your whole .mdp
> file
> to see
> if anyone can spot the underlying issue.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
> <http://vt.edu> | (540)
>
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> -- Quaerendo Invenietis-Seek and you shall discover.
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>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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