[gmx-users] Error with LINC warning

[Justin A. Lemkul]

There are several hundred posts about LINCS warnings in the list archive that 
should provide a starting point.  Also have a look here:

http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

-Justin

vivek sharma wrote:
> Hi there,
> 
> I am running gromacs in parellel with mpi interface..(np 20)
> but it is exiting with the following error in output file
> .
> .
> .
> .Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 1.151530 (between atoms 2685 and 2686) rms 0.187095
> bonds that rotated more than 30 degrees:
> .
> .
> .
> .
> Wrote pdb files with previous and current coordinates
> srun: error: n26: task3: Segmentation fault
> srun: Terminating job
> 
> I am not understanding the error, Can anybody help me in understanding 
> that what does this error indicates ?
> following is the md.mdp file I am using to run simulation. Is there any 
> problem with the parameters ?
> 
> md.mdp..............................................
> title               = trp_drg MD
> cpp                 = /lib/cpp ; location of cpp on SGI
> constraints         = all-bonds
> integrator          = md
> dt                  = 0.02 ; ps !
> nsteps              = 250000 ; total 5000 ps.
> nstcomm             = 1
> nstxout             = 25000 ; output coordinates every 500.0 ps
> nstvout             = 0
> nstfout             = 0
> nstlist             = 5
> ns_type             = grid
> rlist               = 0.9
> coulombtype         = PME
> rcoulomb            = 0.9
> rvdw                = 1.4
> fourierspacing      = 0.12
> fourier_nx        = 0
> fourier_ny        = 0
> fourier_nz        = 0
> pme_order         = 6
> ewald_rtol        = 1e-5
> optimize_fft      = yes
> ; Berendsen temperature coupling is on in four groups
> Tcoupl                = berendsen
> tau_t                 = 0.1         0.1   0.1
> tc-grps               = protein     NDP   sol
> ref_t                 = 300         300   300
> ; 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            = 300.0
> gen_seed            = 173529
> 
> Any suggestion would be of great help..
> 
> With Thanks,
> Vivek
> 
> 
> 
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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

========================================