[gmx-users] Weird structure after minimization (membrane proteinsimulation
alokjain at iitk.ac.in
Wed Jan 30 06:19:41 CET 2008
Dear Mark & Chris,
Thanks a lot for your help.
As both of you suggested I have increased the tolerence limit of the bond
(using VMD, as described by Chris), after increasing the Dynamic bond lenth,
the structure looks fine. So it means that during mimimization, position of
water hydrogens are moved further to their ideal limit. So what could be the
possible reason for that? Is this the problem of my initial structure or
that of mimimization parameters (em.mdp)?
what do you think about my plots from md_run data? Do they look fine or that
could be the root of the problem?
After having checked again I see that I had not got any LINCE warning for
protein atoms. I had got for water molecules only. As per your concern about
the algoritham, possibly this could be due to the report of first few N
LINCE warnings only. I am posting this issue to the developer also, But my
personnel opinion is that this may not be the case because in tpr file
protein comes first followed with water, so if there is any chiral inversion
or LINCE ERROR in protein it should have been reported first (Correct me if
I am wrong).
I was getting LINCE warning in first equilibration run and not in
about " comm_grps = Protein_POP SOL " that was suggested by Dr. Xavier
some time ago.
I will also try " comm_grps = system" and come back to you.
Thanks again for your precious help.
----- Original Message -----
From: "Chris Neale" <chris.neale at utoronto.ca>
To: <gmx-users at gromacs.org>
Sent: Tuesday, January 29, 2008 1:29 AM
Subject: [gmx-users] Weird structure after minimization (membrane
> >Dear All,
> >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
> >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,
> >Best regards,
> >Alok Jain
> >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
> http://i269.photobucket.com/albums/jj58/gromacs/hole-depth-atom1.jpg As 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"
> >top file:
> >; Include forcefield parameters
> >#include "/home/lysine/ffoplsaa.itp"
> >; Include chain topologies
> >#include "Protein_A.itp"
> >#include "Protein_B.itp"
> >#include "Protein_C.itp"
> >#include "Protein_D.itp"
> >#include "pope_opls.itp"
> >; Include water topology
> >#include "tip4p.itp"
> >#ifdef POSRES_WATER
> >; Position restraint for each water oxygen
> >[ position_restraints ]
> >; i funct fcx fcy fcz
> > 1 1 10000 10000 10000
> >; Include generic topology for ions
> >#include "ions.itp"
> >[ system ]
> >; Name
> >protein + POPE + TIP4P water molecules
> >[ molecules ]
> >; Compound #mols
> >Protein_A 1
> >Protein_B 1
> >Protein_C 1
> >Protein_D 1
> >POPE 269
> >SOL 13800
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