Hello gromacs users,

    
           Greetings!

             
                I am working with a drug-enzyme complex. For my complex, I am facing the problem in the energy minimisation step with both steepest followed by  conjugate . Both of these integrators, didn't converge with the given number of steps. I did the energy minimisation using steepest with the following parameters in the em.mdp file:

==========================em.mdp(steep)=============

cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  1000
                                                                               
;
;       Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01
                                                                               
nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

================================================

  I got the follwing result:


Stepsize too small (5.71705e-07 nm)Converged to machine precision,
but not to the requested precision (2000)
                                                                               
Steepest Descents did not converge in 442 steps
  Potential Energy  = -7.01019e+05
Maximum force:  9.58302e+03

============================================
 
             So, I again performed the energy minimisation using the conjugate gradient with the following parameters after the steepest:

============em.mdp(cg)=========
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  cg
nsteps              =  1000
nstcgsteep          =  1000
;
;       Energy minimizing stuff
;
emtol               =  1000
emstep              =  0.01
                                                                               
nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
Pcoupl              =  no
gen_vel             =  no
rvdw                =  1.0
Tcoupl              =  no

=======================


      I got the following output for my CG minimisation:


Negative number for sqrt encountered (-75353886948327424.000000)
Terminating minimization
                                                                               
writing lowest energy coordinates.
                                                                               
Back Off! I just backed up em.trr to ./#em.trr.1#
                                                                               
Conjugate Gradients did not converge in 927 steps
  Potential Energy  = -7.80361e+05
Maximum force:  1.08202e+04
                                                                               
=============


           Please let me know, what is the problem with the energy minimisation. Am I going wrong with any of the parameters in the em.mdp file? Please guide me. Should i proceed with my molecular dynamics with this minimised complex coordinates, or should i further minimize the same? Please guide me.

Thanks in advance!



        "praise the lord!"


With prayers,
prettina


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