[gmx-users] Regarding Production MD error
kirubakaran palani
kirubakaran17 at gmail.com
Sun Aug 19 10:07:32 CEST 2012
Dear EB,
Thanks for your replay..
I will check the above two points and try to do the MD again.
And regarding my system it contains,
title = OPLS Lysozyme MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 15000000 ; 2 * 15000000 = 30000 ps, 30 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
Urs
Kirubakaran P
On Sun, Aug 19, 2012 at 1:22 PM, Emanuel Birru <Emanuel.Birru at monash.edu> wrote:
> It's a LINCS warning relayed to some of the bonding of the atoms, check them they are listed on the warning. Two things that I can suggest is that
> 1. If you are using bigger time steps make it smaller like 1fs.
> 2. If those atoms which make the problem are H atoms makes the heavy atom and rerun the simulation.
>
> If you tell us more about your system you might get more help. You can get More info on the GROMACS website.
>
> Cheers,
> EB
>
>
>
>
> Sent from my iPhone
>
> On 19/08/2012, at 5:41 PM, "kirubakaran palani" <kirubakaran17 at gmail.com> wrote:
>
>> Dear Users,
>>
>> I am running the final MD of my protein ligand complex in 16 processor
>> node for 30ns in gromacs455 version. There, in 9th ns it stops and
>> giving error message like given below. What could be the reason for
>> this and how to rectify this error.
>>
>> Any help will be highly appreciated.
>>
>> Urs,
>>
>> Kirubakaran P
>>
>>
>>
>> Error msg given below,
>>
>> ==================================================================================================
>>
>> Step 4500632, time 9001.26 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000105, max 0.002448 (between atoms 3333 and 3332)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3333 3332 30.3 0.1094 0.1093 0.1090
>>
>> Step 4500659, time 9001.32 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000112, max 0.001661 (between atoms 2217 and 2219)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 34.6 0.1090 0.1091 0.1090
>>
>> Step 4500660, time 9001.32 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000168, max 0.003118 (between atoms 3331 and 3330)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 34.1 0.1091 0.1093 0.1090
>>
>> Step 4500664, time 9001.33 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000120, max 0.002250 (between atoms 3329 and 3328)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 39.4 0.1091 0.1090 0.1090
>>
>> Step 4500665, time 9001.33 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000127, max 0.001588 (between atoms 3333 and 3332)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 35.9 0.1090 0.1090 0.1090
>>
>> Step 4500669, time 9001.34 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000116, max 0.001965 (between atoms 3329 and 3328)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 32.1 0.1091 0.1092 0.1090
>>
>> Step 4500670, time 9001.34 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000149, max 0.002709 (between atoms 3331 and 3330)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 41.6 0.1092 0.1093 0.1090
>>
>> Step 4500671, time 9001.34 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000189, max 0.002999 (between atoms 3327 and 3326)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 36.6 0.1093 0.1093 0.1090
>>
>> Step 4500672, time 9001.34 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000225, max 0.004804 (between atoms 3327 and 3326)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>>
>> Step 4500686, time 9001.37 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000156, max 0.003574 (between atoms 3331 and 3330)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 30.9 0.1094 0.1094 0.1090
>>
>> Step 4500687, time 9001.37 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000161, max 0.002976 (between atoms 3331 and 3330)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 39.3 0.1094 0.1093 0.1090
>>
>> Step 4500688, time 9001.38 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000171, max 0.002600 (between atoms 3329 and 3328)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3331 3330 41.0 0.1093 0.1092 0.1090
>>
>> Step 4500689, time 9001.38 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000127, max 0.002282 (between atoms 3328 and 3327)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3329 3328 36.2 0.1093 0.1091 0.1090
>> 3331 3330 32.4 0.1092 0.1090 0.1090
>>
>> Step 4500690, time 9001.38 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000133, max 0.002643 (between atoms 3331 and 3330)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3329 3328 35.7 0.1091 0.1090 0.1090
>> 3331 3330 30.4 0.1090 0.1087 0.1090
>>
>> Step 4500692, time 9001.38 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000373, max 0.007624 (between atoms 3329 and 3328)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3329 3328 47.9 0.1089 0.1082 0.1090
>>
>> Step 4500693, time 9001.39 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.000149, max 0.003023 (between atoms 3327 and 3326)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3329 3328 48.2 0.1082 0.1093 0.1090
>>
>> Step 4500694, time 9001.39 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.080880, max 2.067793 (between atoms 3329 and 3328)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3329 3328 90.1 0.1093 0.3344 0.1090
>> 3331 3330 90.0 0.1090 0.2852 0.1090
>> Wrote pdb files with previous and current coordinates
>>
>> Step 4500695, time 9001.39 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 490.514956, max 15813.544922 (between atoms 3331 and 3330)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3323 3322 59.0 0.1610 2.3283 0.1610
>> 3326 3323 92.9 0.1616 4.3197 0.1610
>> 3325 3323 88.7 0.1479 2.3003 0.1480
>> 3324 3323 118.7 0.1610 2.2779 0.1610
>> 3327 3326 52.0 0.1362 21.8600 0.1360
>> 1807 1808 90.0 0.1090 0.5027 0.1090
>> 3332 3327 106.4 0.1399 31.1642 0.1390
>> 3328 3327 92.3 0.1403 68.1702 0.1390
>> 3330 3328 89.5 0.1399 34.3474 0.1390
>> 3329 3328 95.1 0.3344 47.7915 0.1090
>> 3336 3330 92.4 0.1405 179.8941 0.1390
>> 3331 3330 89.6 0.2852 1723.7854 0.1090
>> 3334 3332 96.7 0.1392 59.2178 0.1390
>> 3333 3332 121.2 0.1090 10.6428 0.1090
>> 3336 3334 90.0 0.1391 67.5634 0.1390
>> 3335 3334 101.3 0.1091 29.9005 0.1090
>> 3337 3336 96.8 0.1392 151.3580 0.1390
>> 3338 3337 91.6 0.1531 134.4151 0.1530
>> 3344 3338 86.4 0.1530 43.7928 0.1530
>> 3339 3338 101.9 0.1470 37.5223 0.1470
>> 3341 3339 92.7 0.1340 11.1102 0.1340
>> 3340 3339 88.7 0.1000 7.2787 0.1000
>> 3343 3341 105.7 0.1530 2.5647 0.1530
>> 3342 3341 103.6 0.1230 2.6986 0.1230
>> 3346 3344 82.0 0.1340 1.1837 0.1340
>> 3345 3344 81.9 0.1230 0.9566 0.1230
>> 3348 3346 88.9 0.1470 0.6030 0.1470
>> 3347 3346 88.1 0.1000 0.3101 0.1000
>> 3353 3348 82.2 0.1530 0.2466 0.1530
>> 3349 3348 82.9 0.1530 0.2589 0.1530
>> 3350 3349 44.2 0.1530 0.2128 0.1530
>> 3355 3353 36.7 0.1340 0.1797 0.1340
>> 3354 3353 36.8 0.1230 0.1639 0.1230
>> Wrote pdb files with previous and current coordinates
>> --------------------------------------------------------------------------
>> mpirun noticed that process rank 2 with PID 26195 on node node01
>> exited on signal 11 (Segmentation fault).
>>
>>
>> ====================================================================================================
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