[gmx-users] Energy Minimization with Lipid Bilayer

Justin Lemkul jalemkul at vt.edu
Thu Nov 23 23:09:34 CET 2006

Hi Tsjerk,

Thanks for helpful advice.  I decided to re-build my system from scratch, and I
ran energy minimization again.  This still ended badly, with a potential energy
on the order of 10^8.  Better than 10^18, but still not anywhere close to

> My guess is that you've generated severe overlaps. On your starting
> structure (the one you use as input to grompp) run trjconv -s in.gro
> -f in.gro -o out.pdb -pbc inbox

The out.pdb shows that some waters that were initially placed below the DPPC
bilayer (crystal waters from the original structure) are now in a thin slab at
the top of my box.  I'm guessing this is a consequence of pbc, although these
were not applied during my minimization steps.  I centered my system in the box
before beginning (edticonf -c), so I don't know how these residues escaped as a
single unit.

Also problematic is that there are water molecules inside the DPPC bilayer, and
I'm wondering how they got there.  Should I just delete these offending
molecules and try to minimize again?

Any thoughts?  Thanks in advance; I've placed my minim.mdp file below this mail
for your reference.  Hopefully I'm not doing anything obviously wrong, I'm
still very new to Gromacs.


Justin A. Lemkul
Department of Biochemistry
Virginia Tech


title		= 100-ps minimization of DPPC Bilayer with water box ; Title of run

; The following lines tell the program the standard locations where to find
certain files
cpp		= /usr/bin/cpp	; Preprocessor
define		= -DFLEX_SPC
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		= 10		; 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
tau_p           = 5
ref_p           = 1.0

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