[gmx-users] Charge grps and cut-off
saipooja at gmail.com
Sat Jul 17 02:46:34 CEST 2010
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.
; VARIOUS PREPROCESSING OPTIONS
title = NVT simulation (constant number, pressure and
cpp = /lib/cpp
; 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
gen_seed = 9999 ; Seed for (semi) random number
constraints = all-bonds
On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Sai Pooja wrote:
>> 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
>> 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 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
> gmx-users mailing list gmx-users at gromacs.org
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