[gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11
yxc169 at case.edu
Wed Oct 14 04:14:28 CEST 2009
I think your box is too small. try changing them.
On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Nilesh Dhumal wrote:
>> I am trying to equilibrate glucose in water using Gromacs
>> 4.0.5 version. I am geting the error immidiately after the mdrun starts
>> Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is
>> larger than the 1-4 table size 2.400 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> p0_4238: p4_error: interrupt SIGSEGV: 11
>> Killed by signal 2.
> Have you searched the website? You would have undoubtedly found this:
> You should also search the list archive. This problem shows up weekly, if
> not daily sometimes.
> Is the problem in mdp file?
> Nothing seems obviously wrong.
>> Here is my pr.mdp file
>> title = cpeptid position restraining
>> cpp = /usr/bin/cpp
>> constraints = none
>> integrator = md
>> dt = 0.002 ; ps !
>> nsteps = 200000 ; total 1.0 ps.
>> nstcomm = 1
>> nstxout = 10
>> nstvout = 1000
>> nstfout = 0
>> nstlog = 10
>> nstenergy = 10
>> nstlist = 10
>> ns_type = grid
>> rlist = 1.0
>> coulombtype = PME
>> vdwtype = cut-off
>> rcoulomb = 1.0
>> rvdw = 1.4
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 4
>> ewald_rtol = 1e-5
>> optimize_fft = yes
>> ; Berendsen temperature coupling is on
>> Tcoupl = Berendsen
>> tau_t = 0.1
>> tc-grps =system
>> ref_t = 350
>> ; Pressure coupling is on
>> Pcoupl = Berendsen
>> pcoupltype = isotropic
>> tau_p = 0.5
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel = yes
>> gen_temp = 350.0
>> gen_seed = 173529
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> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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Yongchul "Greg" Chung
Dept. of Chemical Engineering, Case Western Reserve University
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