[gmx-users] Weird structure after minimization (membrane protein simulation
alokjain at iitk.ac.in
alokjain at iitk.ac.in
Wed Jan 30 14:52:32 CET 2008
Thanks for your help.
I have also tried the "comm_grps = System" option, and did energy
minimization but after that also water molecular looked like the previous
case (Figure-B, in my previous post).
> >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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