/ Hi
/>/
/>/ I get the following error when using mdrun for a protein in solution.
/>/ I have checked the structure and everything looks fine to me. Could
/>/ you suggested anything else I could do.
/
How did you energy minimze your structure? What was the output of mdrun
during energy minization, especially the last line with Fmax, Epot etc.?
I should look like this:
Step= 48, Dmax= 1.1e-02 nm, Epot= -1.45545e+06 Fmax= 5.58480e+05,
atom= 78754
Step= 49, Dmax= 1.4e-02 nm, Epot= -1.45551e+06 Fmax= 8.80803e+03,
atom= 13032
Step= 50, Dmax= 1.7e-02 nm, Epot= -1.45574e+06 Fmax= 1.60758e+04,
atom= 13032
Jochen
Hi Gaurav,
what is your stepsize during the simulation? what is constrained? And
have you run a minimization before starting the simulation?
hear from you soon
Steffen
-----------------------------------------------------------------------
Hi
I used the initial minimization run using grompp and mdrun using steepest
descent for 400 steps and 0.002 ps as the step size. The constraints are
all-atom.
The following is the output from the log file that was generated after the md.
Any suggestions?
Thanks
Gaurav
--------------- mdrun log file output ------------------
Initializing LINear Constraint Solver
number of constraints is 934
average number of constraints coupled to one constraint is 3.6
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.608377 894 898 0.031756
After LINCS 0.126305 892 894 0.007000
Step -2, time -0.004 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.126305 (between atoms 892 and 894) rms 0.007000
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
898 899 41.6 0.1015 0.0997 0.1010
898 900 38.1 0.1038 0.0984 0.1010
Going to use C-settle (6845 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074
rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Constraining the coordinates at t0-dt (step -1)
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.115310 685 686 0.023558
After LINCS 0.115624 892 894 0.006694
Started mdrun on node 0 Tue Mar 14 04:21:35 2006
Initial temperature: 299.541 K
Step Time Lambda
0 0.00000 0.00000
Grid: 12 x 12 x 12 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
There are 21469 atoms in your xtc output selection
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 10.170899 898 899 0.711794
After LINCS 3.372058 894 895 0.239340
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 3.372058 (between atoms 894 and 895) rms 0.239340
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
883 886 36.7 0.1540 0.2007 0.1529
886 887 36.8 0.1098 0.1474 0.1090
886 888 43.6 0.1099 0.1575 0.1090
886 889 51.7 0.1526 0.2510 0.1529
889 890 60.6 0.1097 0.1917 0.1090
889 891 66.2 0.1096 0.2043 0.1090
889 892 44.6 0.1561 0.0485 0.1463
892 893 55.7 0.1042 0.1304 0.1010
894 895 54.6 0.1221 0.5859 0.1340
894 898 135.9 0.1495 0.4473 0.1340
895 896 77.6 0.1051 0.0671 0.1010
895 897 40.4 0.1011 0.1018 0.1010
898 899 40.0 0.0997 0.3249 0.1010
903 905 40.2 0.1453 0.1959 0.1449
905 906 45.2 0.1093 0.1556 0.1090
905 907 65.6 0.1542 0.3041 0.1529
905 921 35.0 0.1527 0.1990 0.1522
907 908 83.4 0.1099 0.2156 0.1090
907 909 70.1 0.1099 0.1907 0.1090
907 910 43.6 0.1519 0.1400 0.1510
910 911 77.9 0.1408 0.3459 0.1400
910 913 77.5 0.1407 0.3356 0.1400
911 912 80.8 0.1084 0.2512 0.1080
911 915 74.9 0.1405 0.2010 0.1400
913 914 81.8 0.1084 0.2760 0.1080
913 917 65.8 0.1404 0.1278 0.1400
915 916 81.7 0.1082 0.2186 0.1080
915 919 41.0 0.1402 0.1786 0.1400
917 918 82.9 0.1082 0.2569 0.1080
917 919 32.7 0.1402 0.1652 0.1400
919 920 82.3 0.1082 0.1984 0.1080
Constraint error in algorithm Lincs at step 0
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
2.38010e+03 4.15026e+01 8.53343e+02 1.45562e+03 4.52843e+03
LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
1.78128e+05 -3.41925e+05 -3.63116e+04 -1.90849e+05 7.96062e+05
Total Energy Temperature Pressure (bar)
6.05213e+05 4.45994e+03 1.19605e+03
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 2850322.250000 (between atoms 895 and 897) rms 192971.500000
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
869 871
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