Re: Question about equilibration

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Wed Jun 15 2011 - 11:48:06 CDT

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,
Joh*a*n

------------------------------------------------------------------------------------------------------
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
>> >>
>> >>
>> >
>> >
>
>

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