[gmx-users] Re: LINCS Warning using mdrun

[Gaurav Chopra]

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

For the initial mdrun, (i.e. energy min before the actual md) the log 
file output (last part is). After this em step I use grompp with my 
final mdp file and then mdrun where I get the LINCS error.

Thanks
gaurav

Energies (kJ/mol)
          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
   3.35740e+03    1.35497e+03    4.60212e+01    8.38627e+02    1.33998e+03
    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
   4.11813e+03    5.16092e+04   -3.42126e+05   -3.63260e+04   -3.15787e+05
   Kinetic En.   Total Energy    Temperature Pressure (bar)
   0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00

          Step           Time         Lambda
           165      165.00000        0.00000

          Step           Time         Lambda
           166      166.00000        0.00000

          Step           Time         Lambda
           167      167.00000        0.00000

  Energies (kJ/mol)
          Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
   3.35747e+03    1.35504e+03    4.60229e+01    8.38637e+02    1.33998e+03
    Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
   4.11748e+03    5.16092e+04   -3.42126e+05   -3.63260e+04   -3.15788e+05
   Kinetic En.   Total Energy    Temperature Pressure (bar)
   0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00

          Step           Time         Lambda
           168      168.00000        0.00000

          Step           Time         Lambda
           169      169.00000        0.00000

          Step           Time         Lambda
           170      170.00000        0.00000


Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 171 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -3.1578772e+05
Maximum force     =  5.0164816e+04 on atom 897
Norm of force     =  1.1000233e+05

   M E G A - F L O P S   A C C O U N T I N G

  RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
  T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
  NF=No Forces

Computing:                        M-Number         M-Flops  % of Flops
-----------------------------------------------------------------------
Coul(T)                          20.674176      868.315392     1.8
Coul(T) [W3]                      0.311534       38.941750     0.1
Coul(T) + LJ                     19.239903     1058.194665     2.2
Coul(T) + LJ [W3]                 3.200326      441.644988     0.9
Coul(T) + LJ [W3-W3]             78.699237    30063.108534    62.8
Outer nonbonded loop              8.258931       82.589310     0.2
1,4 nonbonded interactions        0.413991       37.259190     0.1
Spread Q Bspline                234.956736      469.913472     1.0
Gather F Bspline                234.956736     2819.480832     5.9
3D-FFT                          723.824532     5790.596256    12.1
Solve PME                        10.687500      684.000000     1.4
NS-Pairs                        214.955143     4514.058003     9.4
Reset In Box                      3.671199       33.040791     0.1
Shift-X                           3.670515       22.023090     0.0
CG-CoM                            1.225386       35.536194     0.1
Bonds                             0.159714        6.867702     0.0
Angles                            0.287622       46.882386     0.1
Propers                           0.030780        7.048620     0.0
RB-Dihedrals                      0.320625       79.194375     0.2
Settle                            2.340990      756.139770     1.6
-----------------------------------------------------------------------
Total                                         47854.835320   100.0
-----------------------------------------------------------------------

              NODE (s)   Real (s)      (%)
      Time:     50.000     50.000    100.0
Finished mdrun on node 0 Wed Mar  8 06:13:35 2006