[gmx-users] Reg. minimization

[David van der Spoel]

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

> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++