[gmx-users] Re: LINCS Warning using mdrun
Yang Ye
leafyoung81-group at yahoo.com
Tue Mar 14 16:15:29 CET 2006
Hi, Gaurav
Try to use another gen_seed number.
Yang Ye
Gaurav Chopra wrote:
>> / 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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