[gmx-users] Charge grps and cut-off
Sai Pooja
saipooja at gmail.com
Sat Jul 17 13:39:39 CEST 2010
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?
Pooja
On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul <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>> 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>>> 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> | (540)
>>
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>> -- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>> -- ========================================
>>
>> 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
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>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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