[gmx-users] Energy Minimization with Lipid Bilayer

[Justin Lemkul]

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

; LINES STARTING WITH ';' ARE COMMENTS
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