[gmx-users] md.mdp query

Antonia V. antonia_haha at hotmail.com
Tue Apr 7 14:44:37 CEST 2009

At the beginning of your md.mdp file you will see the following:

integrator               = steep

With this command you ask GROMACS to energy minimize your system by steepest descent. 
If you want to run a md simulation you will have to change the intergrator to md.
You can read this, and more, in details in the manual.

Good luck

Date: Tue, 7 Apr 2009 17:16:03 +0530
From: bissoyi.akalabya at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] md.mdp query

hello gromacs,
i want to know the changes to be done in md.mdp files for 10 ns.
i am trying to run it but it's showing the following message.

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =     10000000

Step=    0, Dmax= 1.0e-02 nm, Epot= -5.01412e+06 Fmax= 3.66197e+03, atom= 4032
Step=    2, Dmax= 5.0e-03 nm, Epot= -5.01438e+06 Fmax= 2.17491e+04, atom= 4032
Step=    3, Dmax= 6.0e-03 nm, Epot= -5.01456e+06 Fmax= 9.13099e+03, atom= 4032

Step=    5, Dmax= 3.6e-03 nm, Epot= -5.01468e+06 Fmax= 9.44298e+03, atom= 4032
Step=   10, Dmax= 2.7e-04 nm, Epot= -5.01470e+06 Fmax= 8.04093e+03, atom= 4032
Step=   11, Dmax= 3.2e-04 nm, Epot= -5.01472e+06 Fmax= 6.36864e+03, atom= 4032

Step=   12, Dmax= 3.9e-04 nm, Epot= -5.01474e+06 Fmax= 4.35105e+03, atom= 4032
Step=   14, Dmax= 2.3e-04 nm, Epot= -5.01476e+06 Fmax= 3.13319e+03, atom= 4032
Step=   16, Dmax= 1.4e-04 nm, Epot= -5.01478e+06 Fmax= 2.39737e+03, atom= 4032

Step=   18, Dmax= 8.4e-05 nm, Epot= -5.01478e+06 Fmax= 1.98224e+03, atom= 4032
Step=   21, Dmax= 2.5e-05 nm, Epot= -5.01479e+06 Fmax= 1.88313e+03, atom= 4034
Step=   22, Dmax= 3.0e-05 nm, Epot= -5.01479e+06 Fmax= 1.68824e+03, atom= 4032

Step=   23, Dmax= 3.6e-05 nm, Epot= -5.01479e+06 Fmax= 1.50693e+03, atom= 4032
Step=   25, Dmax= 2.2e-05 nm, Epot= -5.01479e+06 Fmax= 1.39532e+03, atom= 4032
Step=   26, Dmax= 2.6e-05 nm, Epot= -5.01480e+06 Fmax= 1.30313e+03, atom= 4032

Step=   27, Dmax= 3.1e-05 nm, Epot= -5.01481e+06 Fmax= 1.12668e+03, atom= 4034
Step=   28, Dmax= 3.8e-05 nm, Epot= -5.01482e+06 Fmax= 9.41676e+02, atom= 4034
Step=   30, Dmax= 2.3e-05 nm, Epot= -5.01483e+06 Fmax= 8.67996e+02, atom= 4032

Step=   31, Dmax= 2.7e-05 nm, Epot= -5.01483e+06 Fmax= 6.80316e+02, atom= 4034
Step=   32, Dmax= 3.2e-05 nm, Epot= -5.01484e+06 Fmax= 5.66923e+02, atom= 4034
Step=   33, Dmax= 3.9e-05 nm, Epot= -5.01485e+06 Fmax= 3.30411e+02, atom= 1881

Step=   35, Dmax= 2.3e-05 nm, Epot= -5.01487e+06 Fmax= 3.12606e+02, atom= 1881
Step=   37, Dmax= 1.4e-05 nm, Epot= -5.01488e+06 Fmax= 3.86990e+02, atom= 92925
Step=   38, Dmax= 1.7e-05 nm, Epot= -5.01489e+06 Fmax= 3.70596e+02, atom= 286823

Step=   40, Dmax= 1.0e-05 nm, Epot= -5.01489e+06 Fmax= 4.65471e+02, atom= 142601
Step=   41, Dmax= 1.2e-05 nm, Epot= -5.01490e+06 Fmax= 4.51394e+02, atom= 155810
Step=   43, Dmax= 7.3e-06 nm, Epot= -5.01490e+06 Fmax= 6.46500e+02, atom= 167601

Step=   47, Dmax= 1.1e-06 nm, Epot= -5.01490e+06 Fmax= 4.30994e+03, atom= 214498
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)

writing lowest energy coordinates.

Back Off! I just backed up traj.trr to ./#traj.trr.12#

Back Off! I just backed up md.pdb to ./#md.pdb.8#

Steepest Descents converged to machine precision in 48 steps,
but did not reach the requested Fmax < 10.

Potential Energy  = -5.0149030e+06
Maximum force     =  6.4650037e+02 on atom 167601
Norm of force     =  7.3590344e+04

Kindly help me in this regard.I am attaching md.mdp file in which i have made the changes.


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