[gmx-users] Problems with molecular dynamic investigation of an cyclic peptide nanotube

[Justin A. Lemkul]

huifang liu wrote:
> Hi, Gromacs users,
>  
> I was caught by a big problem with molecular dynamic investigation of an 
> cyclic peptide nanotube. When i do energy minimization with em.mdp 
> parameter file as follows, it gave out a warning: Warning: 1-4 
> interaction between 135 and 144 at distance larger than 1 nm. I 
> ignored it and went on the next step with pr.mdp as follows, but it 
> crashed with the following information:
>  

Your system is exploding.  Have a look here:

http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off

as well as:

http://wiki.gromacs.org/index.php/blowing_up

-Justin

> 
> Wrote pdb files with previous and current coordinates
> 
> [node1:15777] *** Process received signal ***
> 
> [node1:15777] Signal: Segmentation fault (11)
> 
> [node1:15777] Signal code: Address not mapped (1)
> 
> [node1:15777] Failing at address: 0xba8e28
> 
> [node1:15777] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0]
> 
> [node1:15777] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58]
> 
> [node1:15777] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97]
> 
> [node1:15777] [ 3] mdrun_ompi(force+0x120) [0x4432f0]
> 
> [node1:15777] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb]
> 
> [node1:15777] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf]
> 
> [node1:15777] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc]
> 
> [node1:15777] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd]
> 
> [node1:15777] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
> [0x307851c3fb]
> 
> [node1:15777] [ 9] mdrun_ompi [0x412e8a]
> 
> [node1:15777] *** End of error message ***
> 
> Segmentation fault
> 
>  
> 
> I am extremely puzzed and don't know how to solve this problem. In 
> additon, my previous system runs normally with the same parameter file. 
> 
>  
> 
> ##############em.mdp file
> 
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  none
> integrator          =  steep
> nsteps              =  100
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  2000
> emstep              =  0.01
> 
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> 
>  
> 
>  
> 
>  
> 
> #########pr.mdp
> 
> title               =  Yo
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  2500  ; total 5 ps.
> nstcomm             =  1
> nstxout             =  500
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  500
> nstenergy           =  500
> nstlist             =  5
> ns_type             =  grid
> coulombtype         =  PME
> rlist               =  0.9
> rcoulomb            =  0.9
> rvdw                =  0.9
> fourierspacing      =  0.12
> pme_order           =  4
> optimize_fft        =  yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tc-grps             =   Protein
> tau_t               =   0.1
> ref_t               =    10
> ; Energy monitoring
> energygrps          =  Protein
> ; Pressure coupling is not on
> Pcoupl              =  berendsen
> pcoupltype          =  anisotropic
> tau_p               =  1
> compressibility     =  4.5e-5 4.5e-5 4.5e-5 0 0 0
> ref_p               =  1 1 1 1 1 1
> ; Generate velocites is on at 300 K.
> gen_vel             =  no
> gen_temp            =  300.0
> gen_seed            =  173529
> 
>  
> 
>  
> 
> Look forward to your help. Thanks in advance.
> 
>  
> 
> Huifang 
> 
>  
> 
> 
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> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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