[gmx-users] Weird structure after minimization (membrane protein simulation
chris.neale at utoronto.ca
Mon Jan 28 20:59:59 CET 2008
>I am doing the simulation of POPE lipid + Protein, I did my system
setup using mdrun_hole program. It looks fine to me
(Figure-A). When I was doing energy minimization (using steepest decent
and conjugant gradient algorithm), water molecules diffuse a lot,
structure looks very weird (Figure-B). But only after 1ps mdrun (NVT
ensemble) it comes back to its normal (Figure-C). But during this 1ps I
got lots of LINCE warning, all for water molecules. If I continue my
simulation (till now ~5ns production run) I do not get any problem/warning.
>So I just want to know should I proceed further, or I have to come
back to my initial state and resolve this problem?
>Previously I tried different options by changing value of emtol but I
could not resolve this problem. So I proceeded. By this mail, I am
requesting expert comments from you people. Is it normal to Membrane
simulation or there is some problem in my system? Till now I have not
encountered any problems/warning.
>Eagerly waiting for your reply,
>Thanks a lot for your reply/comments and time. I am using TIP4P water
model, and I really could not understand why it happens, Some of the
bonds of the water molecules are broken down, and after 1ps MD they
make bonds again. Is it not very strange? I have tried to visualize in
different visualization tool but still problem was persisting. I was not
able to implement your suggestion regarding tolerance limit of the
visualization software, I used rasmol, chimera, insightII but could not
found any such option. I am still trying for that, if I could found it,
I will inform you the result after that. I am really worried about
temporary LINCE warning
>which I was getting. Is there any way to resolve this issue?
Use VMD and set your representation to "dynamic bonds", then there is a
sliding bar that determines how to detect bonds.
Easier yet, load your initial (presumable ok) structure from figure A
into VMD, then load in the figure B structure as a new frame
in the original structure. This will draw the representation of fig B
using the topology as determined from fig A.
>I am pasting the em.mdp and my top file below.
>@chris: Thanks for your time spent on investigating on my problem.
Thanks for creating the public album. I am sorry to say I could not get
your statement "In the worst case scenario that I can imagine, temporary
lincs warning could represent a chiral inversion that will never be
resolved and never give you any more warning messages, but would
definitely give you the wrong answer." could you please explain it a
little more (in layman term) because as I think there is no Chiral
center in water so what it
>means by chiral inversion.
Yes, water has no chiral center. But your protein does. In the midst of
all those LINCS warnings,
you might have had one about your protein, and it is even possible that
only the first N LINCS errors
are reported (you could ask a developer about that) so possibly you have
protein angles rotating
too much during minimization steps without knowing it.
Regarding what I mean by a chiral inversion... If forces get too high in
EM, it is entirely possible that
totally unphysical things can happen. To give an MD example, a long time
ago (using CHARMM) I was doing
simulated annealing and taking my structure up to 5000K. At that
temperature, I had some strange rearrangements
where the Ca of a Trp had a "chiral inversion" (perhaps not the correct
term?) in which my L-Trp became D-Trp.
Then upon cooling, the molecule no longer had enough energy to overcome
this L to D barrier of the improper and
note that impropers do not enforce L amino acids, they just hinder L->D
or D->L conversions.
>I have also plotted the two plots to validate my final structure of
mdrun_hole program and uploaded these plots at
I pasted below my em.mdp file. I was using FLEXIBLE TIP4P water molecules.
>define = -DFLEXIBLE
>constraints = none
>integrator = steep
>nsteps = 10000
>; Energy minimizing stuff
>emtol = 100
>emstep = 0.001
>nstcgsteep = 1000
>comm_mode = Linear
>nstcomm = 1
>comm_grps = Protein_POP SOL
>ns_type = grid
>rlist = 0.9
>coulombtype = PME
>rcoulomb = 0.9
>vdw-type = Cut-off
>rvdw = 1.2
>fourierspacing = 0.12
>pme_order = 4
>ewald_rtol = 1e-5
>optimize_fft = yes
>Tcoupl = no
>Pcoupl = no
>gen_vel = no
Are you sure about "comm_grps = Protein_POP SOL" ??
Try with "comm_grps = System"
>; Include forcefield parameters
>; Include chain topologies
>; Include water topology
>; Position restraint for each water oxygen
>[ position_restraints ]
>; i funct fcx fcy fcz
> 1 1 10000 10000 10000
>; Include generic topology for ions
>[ system ]
>protein + POPE + TIP4P water molecules
>[ molecules ]
>; Compound #mols
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