[gmx-users] Energy Minimization with Lipid Bilayer

[Mark Abraham]

Justin Lemkul wrote:
> Hello gmx-users,
> 
> I am having a problem with energy minimization of a DPPC bilayer and solvent.  I
> have searched the archives for a good long while to help solve my problem, but
> so far I have had no luck.  The system I am building consists of the bilayer
> and solvent molecules (water), in preparation for the insertion of a membrane
> protein.  I have successfully done energy minimization on the bilayer with
> crystal waters.  I added additional water molecules to appropriately solvate my
> protein, once it is inserted.  When I try to run energy minimization on my
> solvent (to remove any bad contacts between crystal waters and additional
> solvent molecules, etc), I am consistently met with this error from mdrun:
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  5.9483964e+18
> Maximum force     =            inf on atom 6710
> Norm of force     =            nan

How did you add these new waters? Should your system be periodic? Does 
visualising the start, progress and end of the EM trajectory shed any 
light on what is going wrong?

> My .mdp file is this:
> 
> ; The following lines tell the program the standard locations where to find
> certain files
> cpp             = /usr/bin/cpp  ; Preprocessor
> include         = -I./               ; Directories to include in the topology
> format
> 
> ; Parameters describing what to do, when to stop and what to save
> 
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> dt              = 0.002         ; Time step in ps
> emtol           = 1000.0        ; Stop minimization when the maximum force <
> 10.0 kJ/mol
> emstep          = 0.01          ; Energy step size
> nsteps          = 50000         ; Maximum number of (minimization) steps to
> perform
> xtc_grps        = system        ; Which coordinate group(s) to write to disk
> energygrps      = system        ; Which energy group(s) to write to disk
> 
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 0             ; Frequency to update the neighbor list and long
> range forces
> ns_type         = simple        ; Method to determine neighbor list (simple,
> grid)
> rlist           = 0.9           ; Cut-off for making neighbor list (short range
> forces)
> coulombtype     = cut-off       ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 0.9           ; long range electrostatic cut-off
> rvdw            = 0.9           ; long range Van der Waals cut-off
> pbc             = no            ; Periodic Boundary Conditions (yes/no)
> 
> ; Parameters for temperature and pressure
> tau_t           = 0.1
> tc-grps         = system
> ref_t           = 323
> ref_p           = 1.0

That looks fine, unless you should be periodic.

Mark