Dear gmx users,
I am using mdrun command in pentium-4
redhat linux, job was completed without any errors.
When I use the same files in cluster(redhat
enterprizes OS), I got the following error,
Grid: 14 x 14 x 15 cells
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
Rel. Constraint Deviation: Max between atoms
RMS
Before LINCS inf 6056 6059 nan
After LINCS inf 1 4 nan
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 1 and 4) rms nan
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
1 4 90.0 0.1470 inf 0.1470
2 4 90.0 0.1470 inf 0.1470
3 4 90.0 0.1470 inf 0.1470
4 5 90.0 0.1470 inf 0.1470
..............................................
..............................................
after few lines it is coming as sigmentation fault.
I used grompp command to prepare mdrun input file
(*.tpr) in petium-4 and in cluster, I couldn't get any
warning messages in both cases.
here is my input file:
title = dopc
cpp = /lib/cpp
integrator = md
dt = 0.002
nsteps = 500000
#Out put control parameters
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstxtcout = 0
#neighbor searching parameters
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
#Electrostatic and VdW parameters
coulombtype = PME
pme_order = 4
ewald_rtol = 1e-5
vdwtype = Cut-off
rvdw = 1.0
#Temperature and parameters
tcoupl = berendsen
tc_grps = DOP SOL
tau_t = 0.1 0.1
ref_t = 303 303
#Pressure and parameters
pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 1.0 1.0 1.0 1.0 1.0 1.0
compressibility = 5e-5 5e-5 5e-5 0.0 0.0 0.0
ref_p = 1.0 1.0 1.0 1.0 1.0 1.0
#Constraints parameters
gen_vel = yes
gen_temp = 303
gen_seed = 17532
constraints = all-bonds
constraint_algorithm = lincs
lincs_order = 4
lincs_iter = 1
lincs_warnangle = 30
Can you suggest to solve the problem.
Thank you in advance.
with best regards,
NAGARAJU
MULPURI.
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