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
minimization.
about " comm_grps = Protein_POP SOL " that was suggested by Dr. Xavier
some time ago.
http://www.gromacs.org/component/option,com_wrapper/Itemid,165/
I will also try " comm_grps = system" and come back to you.
Thanks again for your precious help.
Regards,
Alok
----- Original Message -----
From: "Chris Neale" <[EMAIL PROTECTED]>
To: <gmx-users@gromacs.org>
Sent: Tuesday, January 29, 2008 1:29 AM
Subject: [gmx-users] Weird structure after minimization (membrane
proteinsimulation
>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
http://i269.photobucket.com/albums/jj58/gromacs/all-three_final.gif
(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,
>
>Best regards,
>Alok Jain
>
>
>@Mark:
>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.
>
>
>
>
>em.mdp
>----------
>
>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"
Chris.
>
>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
>#endif
>
>; 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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