[gmx-users] Charge grps and cut-off
Justin A. Lemkul
jalemkul at vt.edu
Sat Jul 17 13:54:08 CEST 2010
Sai Pooja wrote:
> If gromacs assumes the aminoacid residues as charge groups by default
> then I have many residues which have 12 atoms since I am using an
> all-atom force field-charmm27(counting H).
>
It doesn't matter how many atoms are in a residue, it matters how many atoms are
assigned to a single charge group and how large the resulting group will be.
> Is there a way to define charge groups?
>
Charge groups are defined in the .rtp file, and you can see which one has 12
atoms in it by looking at your topology and watching the cgnr column. If
pdb2gmx produced this large charge group, I'd suspect that's a problem that
needs to be fixed.
-Justin
> On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <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 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>>>
> <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 <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>
> <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
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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>
> <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> <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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