[gmx-users] Re: LINCS Warning using mdrun

[Gaurav Chopra]

>/ 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