Re: Question about equilibration

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jun 15 2011 - 11:38:17 CDT

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 <http://www.ks.uiuc.edu/%7Ejohanstr>
> 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
> >>
> >>
> >
> >
>

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