[gmx-users] energy minimization

[Mark Abraham]

subarna thakur wrote:
> I am doing the energy minimization of a protein using the following 
> keywords in em.mdp file-
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEX_SPC
> constraints         =  none
> integrator          =  steep
> nsteps              =  3000
> ;
> ;    Energy minimizing stuff
> ;
> emtol               =  1000
> emstep              =  0.01
> 
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1
> coulombtype         =  PME
> rcoulomb            =  1.0
> rvdw                =  1.0
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
> 
> -----------------------------------------------------------------
> I am getting the ouput as following---------
> Steepest Descents converged to machine precision in 67 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -4.0967048e+06
> Maximum force     =  3.7720719e+04 on atom 5530
> Norm of force     =  1.7014005e+02
> -----------------------------
> Can anybody suggest what changes I can make

Well you can play with the EM step size, or see if atom 5530 looks 
unhappy, or you can move on to your equilibration and hope nothing's 
seriously wrong.

Mark