Re: Question about equilibration

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Wed Jun 15 2011 - 11:27:45 CDT

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

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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
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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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