[gmx-users] LINCS error

[Justin A. Lemkul]

aiswarya pawar wrote:
> 
> I get an error like this=
> Step 43230, time 86.46 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    2032   2030   90.0    0.4449   0.2622      0.1000
>    2031   2030   90.0    0.1949   0.1264      0.1000
> Wrote pdb files with previous and current coordinates
> 
> Step 43231, time 86.462 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.066301, max 3.173023 (between atoms 2032 and 2030)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    2032   2030   90.0    0.2622   0.4173      0.1000
>    2031   2030   89.9    0.1264   0.1675      0.1000
> 
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.3
> Source code file: constr.c, line: 176
> 
> Fatal error:
> Too many LINCS warnings (1001)
> If you know what you are doing you can adjust the lincs warning 
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> 
> and my md.mdp file i altered goes like this=
> ; VARIOUS PREPROCESSING OPTIONS
> title                    = Production Simulation
> cpp                      = /lib/cpp
> 
> ; RUN CONTROL PARAMETERS
> integrator               = md
> tinit                    = 0       ; Starting time
> dt                       = 0.002   ; 2 femtosecond time step for integration
> nsteps                   = 2500000        ; Make it 10 ns
> 
> ; OUTPUT CONTROL OPTIONS
> nstxout                  = 500 ; Writing full precision coordinates 
> every nanosecond
> nstvout                  = 500 ; Writing velocities every nanosecond
> nstfout                  = 0     ; Not writing forces
> nstlog                   = 2500  ; Writing to the log file every step
> nstenergy                = 2500  ; Writing out energy information every step
> nstxtcout                = 500  ; Writing coordinates every 5 ps
> energygrps               = Protein Non-Protein
> 
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist                  = 5
> ns-type                  = Grid
> pbc                      = xyz
> rlist                    = 0.9
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype              = Reaction-Field
> rcoulomb                 = 1.4
> epsilon_rf               = 78
> epsilon_r                = 1
> vdw-type                 = Cut-off
> rvdw                     = 1.4
> 
> ; Temperature coupling
> Tcoupl                   = Berendsen
> tc-grps                  = Protein  Non-Protein
> tau_t                    = 0.1      0.1
> ref_t                    = 300      300
> ; Pressure coupling
> Pcoupl                   = Berendsen
> Pcoupltype               = Isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                  = no
> ; OPTIONS FOR BONDS
> constraints              = all-bonds
> constraint-algorithm     = Lincs
> unconstrained-start      = yes
> lincs-order              = 4
> lincs-iter               = 1
> lincs-warnangle          = 30
> 
> 
> how should i rectify this. Please help
> 
> 

Please consult 
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings 
and/or the thousands of posts in the list archive that have been asked and 
answered on this topic.

-Justin

-- 
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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

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