[gmx-users] Re: LINCS Warning using mdrun

[Grazia Daminelli]

Dear Jochen

what do you mean with:

>Better show us the output of your energy minimization. The ouput of your 
>md only shows that your sctructure has some serious problem...like your 
>box is too small or whatever...
>
>Jochen
>
which term is telling you that there are problems?
The bonded terms, which are all positive?
The LJ (SR) which is positive and big?
and what about the LJ-14 and Coulomb-14?

I am asking because the energies given by Guarav are not that different 
from the results I get - and somewhere I have a problem, I know, because 
my md simulations are not stable (but I can't find out the reason)

a comment would be highly appreciated

Grazia



>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
>
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