[gmx-users] Energy Minimization with Lipid Bilayer

Justin Lemkul jalemkul at vt.edu
Sun Nov 19 08:02:48 CET 2006

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

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

; Parameters describing what to do, when to stop and what to save

integrator      = steep         ; Algorithm (steep = steepest descent
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
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,
rlist           = 0.9           ; Cut-off for making neighbor list (short range
coulombtype     = cut-off       ; Treatment of long range electrostatic
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

I apologize if this is a trivial question (I am still a newbie to Gromacs), and
I know that a number of similar issues have been discussed, but I would be
forever grateful for some assistance in getting this issue resolved.

Thanks in advance,

Justin A. Lemkul
Undergraduate Researcher
Department of Biochemistry
Virginia Tech

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