mehmet kıytak wrote:
hi Justin... you were right.. my equilibration is ınsufficient...ı
increase nsteps 50000....200000..now ı recieve this message..
Fatal error:
The Z-size of the box (1.957000) times the triclinic skew factor
(1.000000) is smaller than the number of DD cells (2) times the smallest
allowed cell size (1.000000)
How can ı solve this problem...please help me...
The error is still symptomatic of a crash. Your box is distorting too much and
various algorithms (most notably DD) are crashing.
-Justin
1 Şubat 2012 22:37 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> yazdı:
mehmet kıytak wrote:
hi justin
ı used this mdp. file ..simulation box may be wrong.?..ı used
dodecahedron distance edge 2.0 nm.....
No, that's almost certainly not the problem. Insufficient
minimization/equilibration, or instability due to the use of the
free energy code is more likely. You look to be trying to decouple
the entire system, which could be an unstable process. You haven't
said what you're doing, so I won't hazard a guess at this point.
Please refer to the link I provided and try running without the
free energy code. Otherwise, you're (potentially) trying to solve
several problems at once.
-Justin
; Run control
integrator = sd ; Langevin dynamics
tinit = 0
dt = 0.002
nsteps = 2500000 ; 5 ns
nstcomm = 100
; Output control
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 0
nstenergy = 0
nstxtcout = 0
xtc-precision = 1000
; Neighborsearching and short-range nonbonded interactions
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
; Electrostatics
coulombtype = PME
rcoulomb = 1.0
; van der Waals
vdw-type = switch
rvdw-switch = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-06
epsilon_surface = 0
optimize_fft = no
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps = system
tau_t = 1.0
ref_t = 300
; Pressure coupling is on for NPT
Pcoupl = Parrinello-Rahman
tau_p = 0.5
compressibility = 4.5e-05
ref_p = 1.0
; Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda = 0
foreign_lambda = 0.05
sc-alpha = 0.5
sc-power = 1.0
sc-sigma = 0.3
couple-moltype = system ; name of moleculetype to
decouple
couple-lambda0 = vdw ; only van der Waals
interactions
couple-lambda1 = none ; turn off everything, in
this case only vdW
couple-intramol = no
nstdhdl = 10
; Do not generate velocities
gen_vel = no
; options for bonds
constraints = h-bonds ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 12
1 Şubat 2012 19:41 tarihinde Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>> yazdı:
mehmet kıytak wrote:
hi all...
ı have a problem.. ı got segmentation fault when run nvt
equilibration.. ı use below mdp file
Please post a complete .mdp file. The Unix 'cat' command can be
used to print the contents of the text file, which can then be
copied and pasted into an email.
couple-lambda0 = vdw ; only van der Waals
interactions
couple-lambda1 = none ; turn off everything, in
this case only vdW
couple-intramol = no
nstdhdl = 10
It appears you are trying to do a free energy calculation by
transforming your system. Turn off the free energy code to
determine whether or not this is a source of the problem.
<snip>
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.337002, max 0.559171 (between atoms 1 and 4)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 90.0 0.1006 0.1091 0.1000
1 3 90.0 0.2058 0.1141 0.1000
1 4 90.0 0.3028 0.1559 0.1000
Back Off! I just backed up step3b_n3.pdb to
./#step3b_n3.pdb.1#
Back Off! I just backed up step3b_n4.pdb to
./#step3b_n4.pdb.1#
Back Off! I just backed up step3c_n2.pdb to
./#step3c_n2.pdb.1#
Back Off! I just backed up step3c_n3.pdb to
./#step3c_n3.pdb.1#
Back Off! I just backed up step3c_n4.pdb to
./#step3c_n4.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault
mkiytak@babil:~
PLEASE HELP ME...
LINCS warnings are the most common error reported to this list.
Please refer to the following pages for help:
http://www.gromacs.org/____Documentation/Errors#LINCS.____2fSETTLE.2fSHAKE_warnings
<http://www.gromacs.org/__Documentation/Errors#LINCS.__2fSETTLE.2fSHAKE_warnings>
<http://www.gromacs.org/__Documentation/Errors#LINCS.__2fSETTLE.2fSHAKE_warnings
<http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings>>
If you still can't find your answer, refer to the list
archive. As
I said, such errors are commonly reported. Surely you'll find
something useful. The only thing that can be said right now
is that
your system is unstable. Either you need better minimization or
equilibration (or both), your .mdp settings are incorrect, or the
free energy code is causing an instability (which is a symptom of
the first two points, it does not suggest the free energy code is
not working).
-Justin
-- ==============================____==========
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Virginia Tech
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
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Virginia Tech
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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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