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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