AW: [gmx-users] Not able to continue with Equilibration
Rausch, Felix
frausch at ipb-halle.de
Thu Mar 29 11:40:14 CEST 2012
Hello,
The results of the energy minimization look reasonable. Nevertheless, you should (visually) check your equilibration starting structure for problems (e.g. clashes that could not be solved by EM). It would be a good idea to concentrate on the atom numbers given in the error messages.
To prevent the "exploding" system during equilibration, reducing the time step may be a good idea. Or you could start with a short NVT run first to equilibrate the temperature before switching to NPT. Furthermore, the coupling of ions in a single thermostat group is in general not a good idea (search the mailing list for many discussions about this topic).
Good luck.
Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im Auftrag von Hendry
Gesendet: Donnerstag, 29. März 2012 11:25
An: Discussion list for GROMACS users
Betreff: [gmx-users] Not able to continue with Equilibration
Hi,
I am using Gromacs 4.5.4. After successful minimization by SD, I continued with equilibration step but I got the below errors. I tried many times with different parameters but the problem still persists. I have given errors and md parameters of equilibration step below. I have also provided my minimization output at the end. Could you provide some suggestions what went wrong?.
Many thanks
Sincerely
Hendry
Errors:
Warning: 1-4 interaction between 2969 and 2974 at distance 5.543 which is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 92.242942, max 9194.071289 (between atoms 3025 and 3024)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2987 2973 106.3 1.3892 7.3433 0.1530
2974 2973 174.8 1.1940 7.7482 0.1530
2975 2974 79.9 0.1865 1.4460 0.1530
2978 2975 98.5 0.1423 0.6164 0.1390
2982 2978 86.1 0.1421 0.6512 0.1390
2979 2978 89.8 0.1114 5.2456 0.1090
2989 2987 132.2 0.1781 2.6697 0.1330
2988 2987 142.2 0.2284 2.7180 0.1230
2971 2969 62.9 7.0921 3.5084 0.1330
2970 2969 88.1 6.8598 4.7791 0.1230
2973 2971 120.6 2.8109 8.8274 0.1470
2972 2971 165.6 2.0293 6.9953 0.1000
3016 3013 103.1 0.5628 65.6450 0.1390
3014 3013 39.0 0.3331 5.0018 0.1330
3017 3014 81.6 0.1827 57.9252 0.1330
3015 3014 77.9 0.0752 6.3613 0.1090
3020 3016 81.3 2.2255 79.7378 0.1390
3019 3016 100.9 0.4862 54.4883 0.1390
3019 3017 79.3 0.1679 57.8415 0.1330
3018 3017 94.5 0.1686 66.3440 0.1000
3022 3019 87.7 0.5657 7.7539 0.1390
3026 3022 104.5 0.8085 54.9923 0.1390
3023 3022 87.4 0.6108 5.0641 0.1090
2968 2964 174.1 1.5617 5.1413 0.1470
2965 2964 59.5 5.2178 4.0658 0.1470
2969 2965 35.5 7.6693 2.9000 0.1530
2966 2965 137.3 5.3225 4.6157 0.1530
2967 2966 150.3 1.6016 1.7332 0.1530
2968 2967 72.4 0.1685 1.8310 0.1530
3026 3024 94.8 0.8572 96.6156 0.1390
3025 3024 89.9 0.6811 1002.2628 0.1090
3027 3026 108.0 1.1638 47.5384 0.1090
2991 2989 138.2 0.2045 0.6556 0.1470
2990 2989 157.0 0.1236 0.7213 0.1000
2998 2991 89.9 0.1961 0.9471 0.1530
2992 2991 79.5 0.1931 0.5434 0.1530
2993 2992 49.8 0.1577 0.1862 0.1530
3000 2998 84.9 0.1463 0.5492 0.1330
2999 2998 83.3 0.1346 0.5372 0.1230
3002 3000 44.2 0.1535 0.2150 0.1470
3003 3002 31.6 0.1548 0.1834 0.1530
3009 3007 62.4 0.1507 0.3181 0.1330
3008 3007 44.1 0.1280 0.1578 0.1230
3011 3009 80.3 0.2401 1.9894 0.1470
3010 3009 82.9 0.1141 0.3157 0.1000
3028 3011 85.2 0.2391 1.9233 0.1530
3012 3011 97.9 0.3034 4.9831 0.1530
3013 3012 82.4 0.3759 7.3991 0.1530
3024 3020 85.6 2.4674 98.3412 0.1390
3021 3020 81.0 1.2452 66.1375 0.1090
3030 3028 88.9 0.1492 0.2673 0.1330
3029 3028 61.2 0.1379 0.2407 0.1230
49372 49371 89.5 0.1000 221.0566 0.1000
49373 49371 92.4 0.1000 170.7231 0.1000
2956 2954 153.4 0.1550 3.5621 0.1470
2955 2954 135.5 0.1246 0.8967 0.1000
2962 2956 76.6 0.7151 5.0532 0.1530
2957 2956 178.7 0.1220 3.9773 0.1530
2958 2957 155.0 0.2036 1.2639 0.1530
2961 2959 34.5 0.1265 0.1186 0.1250
2960 2959 30.4 0.1264 0.1346 0.1250
2964 2962 114.9 1.7422 7.9205 0.1330
2963 2962 156.9 0.4832 6.1127 0.1230
53158 53157 90.0 0.1000 0.1575 0.1000
53159 53157 90.0 0.1000 0.1747 0.1000
53386 53385 90.0 0.1000 0.1537 0.1000
53387 53385 56.5 0.1000 0.0962 0.1000
2954 2952 68.7 0.1615 0.7870 0.1330
Back Off! I just backed up step1b_n2.pdb to ./#step1b_n2.pdb.1#
Back Off! I just backed up step1c_n2.pdb to ./#step1c_n2.pdb.1#
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, VERSION 4.5.4
Source code file: pme.c, line: 538
Fatal error:
10 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"They Were So Quiet About It" (Pixies)
Error on node 2, will try to stop all the nodes
Halting parallel program mdrun on CPU 2 out of 4
gcq#37: "They Were So Quiet About It" (Pixies)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 30681 on
node ymu039-107 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
Equilibration parameters
title = TM1 in a POPC bilayer at 100K
cpp = /lib/cpp
integrator = md
define = -DPO1000
; Output
dt = 0.002 ; ps !
nsteps = 100000 ; total 200 ps.
nstcomm = 1
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 500
nstenergy = 500
nstxtcout = 500
xtc_precision = 1000
; Electrostatics and VdW
nstlist = 5
pbc = xyz
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
fourierspacing = 0.16
pme_order = 4
rvdw = 1.4
constraints = all-bonds
optimize_fft = yes
constraint-algorithm = lincs
lincs-order = 4
lincs_iter = 1
; berendsen temperature coupling
Tcoupl = berendsen
tc-grps = Protein POPC SOL CL
tau_t = 0.1 0.1 0.1 0.1
ref_t = 100 100 100 100
; Energy monitoring
energygrps = Protein POPC SOL CL
; Isotropic pressure coupling
pcoupl = parrinello-rahman
pcoupltype = semiisotropic
tau_p = 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Generate velocity is on 100K
gen_vel = yes
gen_temp = 100.0
gen_seed = 173529
SD minimization ouput:
Steepest Descents converged to Fmax < 1000 in 23239 steps
Potential Energy = -1.0507182e+06
Maximum force = 9.8500549e+02 on atom 5087
Norm of force = 2.4736889e+01
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