[gmx-users] Re: Minimization

Gia Maisuradze gia at chem.unr.edu
Mon Oct 2 01:36:27 CEST 2006


I am trying to minimize the intermediate of dimeric hemoglobin. First I 
minimized structure by a steepest descents minimization and got following 

 Steepest Descents converged to machine precision in 966797 steps,
but did not reach the requested Fmax < 1e-05.
Potential Energy  = -4.14694118635162e+04
Maximum force     =  4.53760075753937e-02 on atom 212
Norm of force     =  1.13978746433984e-01

Now I want to use the output from steepest descents minimization to perform 
l-bfgs minimization, since my final goal is normal mode analysis.

To run steepest descents minimization I have used:
grompp_d -f em.mdp -c 1d2o.gro -p 1d2o.top -o 1d2o.tpr
mdrun_d -s 1d2o.tpr -o 1d2o_em.trr -c 1d2o_em.gro -g 1d2o_em.log -e 

For l-bfgs minimization I am using:

grompp_d -f lbfgs.mdp -c 1d2o_em.gro -p 1d2o.top -o 1d2o_lbfgs.tpr -t 
1d2o_em.trr -e 1d2o_em.edr
mdrun_d -s 1d2o_lbfgs.tpr -o 1d2o_lbfgs.trr -c 1d2o_lbfgs.gro -g 
1d2o_lbfgs.log -e 1d2o_lbfgs.edr -v

After running the first message is saying following:

Low-Memory BFGS Minimizer:
   Tolerance (Fmax)   =  1.00000e-05
   Number of steps    =      5000000
Using 10 BFGS correction steps.

   F-max             =  2.21999e+03 on atom 2981
   F-Norm            =  9.87438e+03

Step 0, Epot=-4.147040e+04, Fnorm=1.031e+02, Fmax=2.219e+03 (atom 2981)
Step 1, Epot=-4.147356e+04, Fnorm=1.031e+02, Fmax=2.218e+03 (atom 2981)
Step 2, Epot=-4.147683e+04, Fnorm=1.031e+02, Fmax=2.217e+03 (atom 2981)
Step 3, Epot=-4.147742e+04, Fnorm=1.031e+02, Fmax=2.217e+03 (atom 2981)

The maximum force from steepest descents minimization was 
4.53760075753937e-02. Why do I get 2.21999e+03?

Thanks in advance,



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