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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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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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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--
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--
========================================
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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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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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