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,
Tsjerk
On 11/23/06, Justin Lemkul <[EMAIL PROTECTED]> 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
; 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
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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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