C.RAMYA wrote:
Hello,
I am trying to study a mutant lipase molecule. The complex[molecule +
spc water box] has shown +6 charge so i have neutralized the system
using genion. After that i am trying to minimize this.
The mdrun program gets done fine.. but i am having some doubts.
In the log file i do not get values for each step.. as you can see in step
3 and 5 given below [but this is case with many steps..n not in any
regular pattern] :
" Step Time Lambda
3 3.00000 0.00000
Step Time Lambda
4 4.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.49416e+02 1.23777e+03 7.23143e+01 1.73961e+03 3.47387e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
1.86156e+04 8.90799e+04 -5.95683e+05 -9.39925e+04 -5.75307e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda
5 5.00000 0.00000
Step Time Lambda
6 6.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
2.06581e+02 1.18779e+03 7.22623e+01 1.73397e+03 3.45845e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
1.86006e+04 8.90886e+04 -5.95711e+05 -9.39880e+04 -5.75351e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda
7 7.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. LJ-14
1.95651e+02 1.18846e+03 7.23920e+01 1.73374e+03 3.43895e+03
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
1.85910e+04 8.91156e+04 -5.95729e+05 -9.39764e+04 -5.75369e+05
Kinetic En. Total Energy Temperature Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
This is a run with 0.5 ps timestep and no. of steps as 1000 using
steep and PME interactions.[other options are default]
I just wanted to confirm is there any specific reason for this..or is
it fine??
and the final output is -
"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 889 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -5.8063038e+05
Maximum force = 4.5843417e+02 on atom 418
Norm of force = 1.7805715e+03 "
I have read about similar outputs in some papers... but i am actually
not clear if it is required to re-minimize with some changes or is it
fine??
Thanks,
Ramya.
http://wiki.gromacs.org
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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