From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Wed Jun 15 2011 - 13:16:00 CDT
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
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