[gmx-users] Weird structure after minimization (membrane protein simulation)

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jan 30 18:58:34 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).

Thanks for trying that, I guess it was not the problem. As you  
mentioned on another post, 2.5A is way to large and this is indicative  
of problems. I did see your make_hole plots and the general features  
look fine. I think that my second step of hole making was with a  
significantly larger force (1000?) but i don't have my notes with me.

Send me your files off-list and I will take a look. chris.neale at utoronto.ca
.top (all... there should be one with and one without the protein)
.itp (e.g. "Protein_D.itp" and any other modified ffoplsaanb.itp?)
.mdp (all)
.gro (only the first one)

If you don't want to share your files then one thing that I like to do  
to debug is to save the coordinates every single step to the .xtc and  
then you load the initial .gro into vmd then load the .xtc into that  
structure and watch carefully and see what is going on when things  
start looking strange. (PS, do that anyway even if you do send me the  
files please).

Finally, as I believe that Mark already touched on, check the order of  
atoms as they are defined in the [molecules] section of your .top file  
as compared to your .gro file.

Chris.

>
> Regards,
> Alok
>
>>  >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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>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 30 Jan 2008 09:07:43 -0500
> From: "Myunggi Yi" <myunggi at gmail.com>
> Subject: Re: [gmx-users] Turn off the diheral energy
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> 	<ef0ebd150801300607k3a57f2dax5a31c60853cd5b64 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you so much.
>
>
> On Jan 30, 2008 2:57 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
>> Hi Myunggi Yi,
>>
>> >
>> > Mixing force fields is an intrinsically bad idea. See
>> > http://wiki.gromacs.org/index.php/Parameterization
>> >
>>
>> I second that...
>>
>> > > Is it possible to turn off dihedral energy (proper and improper) for a
>> > > certain molecule?
>> > > If yes, then how can I do this?
>> >
>> > Comment out these parts of your topology file.
>> >
>>
>> You can do this easily by enclosing the dihedral section with an
>> #ifdef ... #endif block, and use a control #define statement upstream
>> of it:
>>
>> #define INCLUDE_DIHEDRALS
>>
>> #ifdef INCLUDE_DIHEDRALS
>> [ dihedrals ]
>> ...
>> ...
>> ...
>> #endif
>>
>> This even allows you to control it through the .mdp file, including the
>> line
>>
>> define = -DINCLUDE_DIHEDRALS
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
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>>
>
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi
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