[gmx-users] Charge grps and cut-off
Sai Pooja
saipooja at gmail.com
Sat Jul 17 13:22:43 CEST 2010
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
; 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> 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>> 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> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
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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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
--
Quaerendo Invenietis-Seek and you shall discover.
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