Re: Question about equilibration

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Jun 15 2011 - 14:18:43 CDT

ok, then measure the RMSD from the structure obtained after the heating.
My point is that you measure the RMSD for the total structure and each
helix individually to understand whether the helices are moving with
respect to each other as rigid bodies or also undergoing conformational
changes.

Gianluca

On Wed, 15 Jun 2011, Richard Wood wrote:

> Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated structure
> is at "300 K"?  That's why we "heat" them up and equilibrate before we run MD.
>
> Richard
>
> ___________________________________________________________________________________________
> From: Gianluca Interlandi <gianluca_at_u.washington.edu>
> To: Richard Wood <rwoodphd_at_yahoo.com>
> Cc: johanstr_at_ks.uiuc.edu; snoze pa <snoze.pa_at_gmail.com>; namd-l_at_ks.uiuc.edu
> Sent: Wed, June 15, 2011 2:03:57 PM
> Subject: Re: namd-l: Question about equilibration
>
> Why not plotting the RMSD from the X-ray structure for the total complex and each helix
> independently?
>
> Gianluca
>
> On Wed, 15 Jun 2011, Richard Wood wrote:
>
> > Right, as one can have a "good" RMSD, but a terrible structure.
> >
> > Richard
> >
> >__________________________________________________________________________________________
> _
> > From: johan strumpfer <johanstr_at_ks.uiuc.edu>
> > To: Richard Wood <rwoodphd_at_yahoo.com>
> > Cc: snoze pa <snoze.pa_at_gmail.com>; namd-l_at_ks.uiuc.edu
> > Sent: Wed, June 15, 2011 1:22:56 PM
> > Subject: Re: namd-l: Question about equilibration
> >
> > Indeed, hence my suggestion: in reaching a plateau in the rmsd you
> > find a stable structure to start from for 'production' runs / use as
> > point of comparison. Of course, the difference between this structure
> > and the crystal structure is possibly also of interest - it really
> > depends on the investigation.
> >
> > Cheers,
> > Johan
> >
> > On 6/15/11, Richard Wood <rwoodphd_at_yahoo.com> wrote:
> > > The reason I say this is because a crystal structure of a protein (which I
> > > believe he's starting from) is not a realistic structure, so if you're going
> > > to
> > > compare an equiibrated structure from a dynamics run to that, you could be
> > > asking for trouble.
> > >
> > > Richard
> > >
> > >
> > >
> > >
> > > ________________________________
> > > From: johan strumpfer <johanstr_at_ks.uiuc.edu>
> > > To: Richard Wood <rwoodphd_at_yahoo.com>
> > > Cc: snoze pa <snoze.pa_at_gmail.com>; namd-l_at_ks.uiuc.edu
> > > Sent: Wed, June 15, 2011 1:10:10 PM
> > > Subject: Re: namd-l: Question about equilibration
> > >
> > > The total energy stabilises usually before the structure has
> > > stabilised. It has happened to me quite often that the total energy
> > > fluctuates about a well defined mean by 1 ns, but the rmsd is not yet
> > > stable and only plateau's after 5-10 ns. It is very much dependent on
> > > your starting set up.
> > >
> > > Cheers,
> > > Johan
> > >
> > > On 6/15/11, Richard Wood <rwoodphd_at_yahoo.com> wrote:
> > >> Wouldn't the total energy be a better deterministic tool as to whether or
> > >> not
> > >> you have equilibrated?
> > >>
> > >> Richard
> > >>
> > >>
> > >>
> > >>
> > >> ________________________________
> > >> From: johan strumpfer <johanstr_at_ks.uiuc.edu>
> > >> To: snoze pa <snoze.pa_at_gmail.com>
> > >> Cc: namd-l_at_ks.uiuc.edu
> > >> Sent: Wed, June 15, 2011 11:48:06 AM
> > >> Subject: Re: namd-l: Question about equilibration
> > >>
> > >> Snoze,
> > >>
> > >> You are the only one who can really decide that. Proteins move
> > >> stochastically,
> > >> they do not stay in one conformation, even simple helices. They are
> > >> influenced
> > >> by the other proteins and the environment surrounding them, which is
> > >> usually
> > >> not
> > >> symmetric. As I said before, equilibration runs need to be longer usually:
> > >> look
> > >> at your rmsd as a function of time and when it reaches a plateau, then you
> > >> may
> > >> be in a better position to say whether your structure is equilibrated.
> > >> Whatever
> > >> kinks or deformation are present, you will need to look at the structure,
> > >> at
> > >> the
> > >> interactions and justify them for yourself.
> > >>
> > >> Cheers,
> > >> Johan
> > >>
> >>>----------------------------------------------------------------------------------------
>
> > --------------
> > >>-
> > >>
> > >> Johan Strumpfer:        johanstr_at_ks.uiuc.edu
> > >> www.ks.uiuc.edu/~johanstr
> > >> Theoretical and Computational Biophysics Group
> > >> 3115 Beckman Institute
> > >> University of Illinois at Urbana-Champaign
> > >> 405 N. Mathews
> > >> Urbana, IL 61801, USA
> >>>----------------------------------------------------------------------------------------
>
> > --------------
> > >>-
> > >>
> > >>
> > >>
> > >>
> > >> On Wed, Jun 15, 2011 at 11:38 AM, snoze pa <snoze.pa_at_gmail.com> wrote:
> > >>> Hi John and NAMD users,
> > >>>
> > >>>  Thanks for your reply. My question was related to the deformation of
> > >>> protein during equilibration. First part of the equilibration for 1ns,
> > >>> when
> > >>> I used harmonic constrain went well. I don't see  big structural changes.
> > >>> But when I remove the harmonic constraint and equilibrate further the
> > >>> system
> > >>> for 1ns then till 600 ps i don't see any big change in the structure
> > >>> except
> > >>> the large kink that deform the top part of the two helices in last 300
> > >>> ps.
> > >>> All three helices have similar sequences and they are symmetric in
> > >>> structure. Theoretically all three will show deformed kinked region in
> > >>> top
> > >>> but only two are showing it.
> > >>>
> > >>> So question was: is it okey to have such large movement during
> > >>> equilibration(knowing the fact that protein is symmetric)?  or do you
> > >>> think
> > >>> I have to run it more to see if there are more structural changes before
> > >>> running full MD simulation.
> > >>>
> > >>> Thank you,
> > >>>
> > >>> S
> > >>>
> > >>>
> > >>> On Wed, Jun 15, 2011 at 11:27 AM, johan strumpfer <johanstr_at_ks.uiuc.edu>
> > >>> wrote:
> > >>>>
> > >>>> It looks like a totally reasonable structure to me, but I have no idea
> > >>>> what you are working with, how you've set the system up or what it is
> > >>>> expected to do. You are the only one that can really decide whether
> > >>>> the deformation makes sense and what it's implications are.
> > >>>>
> > >>>> It is not possible for someone to look at your structure and say
> > >>>> whether some deformation is problematic or not, unless they are very
> > >>>> familiar with it or it is clearly a physical impossibility.
> > >>>>
> > >>>> Cheers,
> > >>>> Johan
> > >>>>
> > >>>>
> >>>>>--------------------------------------------------------------------------------------
>
> > ----------------
> > >>>>
> > >>>>-
> > >>>> Johan Strumpfer:        johanstr_at_ks.uiuc.edu
> > >>>>  www.ks.uiuc.edu/~johanstr
> > >>>> Theoretical and Computational Biophysics Group
> > >>>> 3115 Beckman Institute
> > >>>> University of Illinois at Urbana-Champaign
> > >>>> 405 N. Mathews
> > >>>> Urbana, IL 61801, USA
> > >>>>
> >>>>>--------------------------------------------------------------------------------------
>
> > ----------------
> > >>>>
> > >>>>-
> > >>>>
> > >>>>
> > >>>>
> > >>>> On Wed, Jun 15, 2011 at 11:20 AM, snoze pa <snoze.pa_at_gmail.com> wrote:
> > >>>> > Please find the link to check the deformed protein
> > >>>> >
> > >>>> > http://img10.imageshack.us/i/deform.png/
> > >>>> >
> > >>>> > On Wed, Jun 15, 2011 at 11:07 AM, snoze pa <snoze.pa_at_gmail.com> wrote:
> > >>>> >>
> > >>>> >> Dear NAMD Users,
> > >>>> >>
> > >>>> >>
> > >>>> >> I need some explanation regarding my protein equilibration. I see my
> > >>>> >> protein gets deformed during the equilibration. Do you think it is
> > >>>> >> okey?
> > >>>> >>
> > >>>> >> To add one more note about the protein deformation. First I used
> > >>>> >> harmonic
> > >>>> >> constrained during the equilibration. Then the restrain were removed
> > >>>> >> and
> > >>>> >> protein was again equilibrated. I am getting deformation after
> > >>>> >> removing
> > >>>> >> harmonic constraints. In this step during first 600 ps it is fine but
> > >>>> >> last
> > >>>> >> 300 ps the protein is getting deformed.
> > >>>> >>
> > >>>> >> I will highly appreciate your help.
> > >>>> >>
> > >>>> >> Thank you
> > >>>> >>
> > >>>> >> S
> > >>>> >>
> > >>>> >>
> > >>>> >
> > >>>> >
> > >>>
> > >>>
> > >
> > >
> > > --
> > > ----------------------------------------------------------------
> > > Johan Strumpfer (johanstr_at_ks.uiuc.edu)
> > > Theoretical and Computational Biophysics Group
> > > 3115 Beckman Institute
> > > University of Illinois at Urbana-Champaign
> > > 405 N. Mathews
> > > Urbana, IL 61801, USA
> > >
> >
> >
> > --
> > ----------------------------------------------------------------
> > Johan Strumpfer (johanstr_at_ks.uiuc.edu)
> > Theoretical and Computational Biophysics Group
> > 3115 Beckman Institute
> > University of Illinois at Urbana-Champaign
> > 405 N. Mathews
> > Urbana, IL 61801, USA
> >
> >
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>                     +1 (206) 685 4435
>                     http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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