[gmx-users] Energy Minimization with Lipid Bilayer

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 24 09:46:06 CET 2006

Hi Justin,

The problem could well be caused by the waters inside the bilayer. Try
removing them. I guess that all this is a consequence of pbc.
Translating a system (centering it in the box) doesn't really change
anything, bad pbc will be bad pbc. That is to say, it's not really the
pbc that's bad, but the atoms you added may be inside the bilayer of a
periodic image of your system, and consequently mapped to the inside
of the bilayer in your original system. You have to make sure that you
don't generate any overlaps in the input. Probably the best way to
check is to run genconf right after you've added the additional
solvent. genconf -nbox 2 2 2 will copy your system two times in each
direction, allowing you to view a set of periodic images. Check for
overlaps there.

Hope it helps,


On 11/23/06, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> acceptable.
> > 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
> Justin A. Lemkul
> Department of Biochemistry
> Virginia Tech
> -----------------
> minim.mdp
> 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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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