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