Re: Question about equilibration

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Wed Jun 15 2011 - 13:22:56 CDT

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

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