I may have discovered the solution to my own problem, so I'll post it here just
as a follow-up. It appears that inflation of a POPE bilayer causes extremely
favorable interactions within the PE headgroup, causing the amine moiety to
collapse into the phosphate. This generates the near infinite forces that I'm
seeing. I guess somehow the minimization algorithm still finds this
electrostatic interaction to be somehow favorable, since the potential is
plummeting.
I suspect that the EM procedure cuts out because the potential is dropping too
fast for the system to handle, hence why I'm seeing that the system has
converged to machine precision. Maybe the numbers are getting to heavy for my
poor computer's memory :)
Just a few thoughts.
-Justin
Justin A. Lemkul wrote:
Hi all,
I'm preparing a few membrane protein systems using the InflateGRO script
from Tieleman's site. The bilayer consists of 340 POPE lipids, using
structures and topologies from the same site. I've prepared several
systems (with other lipids) using the methodology described, but am
running into some very strange behavior with the POPE system.
I scaled the coordinates for the lipids by a factor of 4 and attempted a
steepest descents minimization, my usual procedure. This step is
essentially an in vacuo minimization of scaled lipids in the presence of
a protein. The potential energy decreases nicely, and levels off.
Suddenly, the potential plummets again, after which mdrun cuts out,
reporting that it has converged to machine precision (although it has
not reached my desired Fmax < 1000). The forces were incredibly large
(greater than 10^11), so there is definitely a problem with the system
that I have yet to figure out.
What troubles me is that mdrun believes the steepest descents algorithm
has converged, when clearly it has not. I have posted an image here to
illustrate the potential energy:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Images/Gromacs/weird_energy.jpg
Conjugate gradients does not give the same result, instead converging to
a potential energy of roughly -4 x 10^5, a reasonable magnitude, given
the size of the system. The forces, however, remain large (10^5 or so),
indicating I probably still have some clashes to resolve.
Still I am troubled by the steepest descents result. Is this indicative
of some problem? I usually use steepest descents, and have never had a
problem with it before. I see the same result in serial or parallel (on
2 CPU's of my dual core laptop), using single-precision GMX 3.3.3.
Thanks for reading yet another long email from me. The .mdp file I used
for steepest descents (that gives the weird behavior) is below. The
behavior persists even if I lower emtol and emstep, it just takes a bit
longer to arrive at the same conclusion :)
-Justin
=======em.mdp========
; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run
; Run control
cpp = /usr/bin/cpp ; Preprocessor
define = -DSTRONG_PR
include = -I../ ; Directories to include in the topology
format
; Parameters describing what to do, when to stop and what to save
integrator = steep
emtol = 1000.0 ; Stop minimization when Fmax < 1000
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of steps
energygrps = system ; Which energy group(s) to write to disk
; Neighbor searching and electrostatics
nstlist = 1
ns_type = simple
rlist = 1.0
coulombtype = cut-off
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
=======================
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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