[gmx-users] segmantation default
mehmet kıytak
mehmetkiytak at gmail.com
Wed Feb 1 21:34:21 CET 2012
hi justin
ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron
distance edge 2.0 nm.....
; 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 <jalemkul at 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 at 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>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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