Re: SMD restrain point in NAMD

From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Aug 04 2009 - 14:45:39 CDT

Gianluca, Thank you for your feedback. I am following the right
tutorial sent also by you but got confused with the paragraph of the
paper. Also in same paragraph, they mentioned a force constant of 414
but down eight lines it says k=10K_BT/A^2.

Regards
s

On Tue, Aug 4, 2009 at 1:09 PM, Gianluca
Interlandi<gianluca_at_u.washington.edu> wrote:
> The best is if you go through the tutorial:
>
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix.pdf
>
> Section 3, in particular 3.2
>
> and read also the documentation:
>
> http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/node41.html
>
> The paper you mentioned is from 1999 and I think that NAMD has been updated
> since than and SMD is implemented in the code of the later NAMD releases. So
> doing SMD should be more straightforward now.
>
> Gianluca
>
> On Tue, 4 Aug 2009, snoze pa wrote:
>
>> Dear NAMD/SMD users,
>>
>> I was going through one of the original paper related to SMD
>> simulation
>> http://proteomics.bioengr.uic.edu/papers/1999/1999-unfold-protein.pdf
>> from Dr. Schulten group. In this paper at page 455, first paragraph
>> they are discussing about the restrain point movement as
>>
>> "To realize a movement of the restraining point with nearly constant
>> velocity, the position of the restraining point was changed every 100
>> fs by v t, e.g., 0.05 . The 0.05 stepwise movement of the
>> restraining point is much smaller than the fluctuation of typical
>> protein atoms in a 300 K MD simulation, 1 , so this implementation
>> should not cause an artifact. "
>>
>>
>> How can we set this "the position of the restraining point was changed
>> every 100 fs by v t" automatically in the NAMD configuration file. I
>> will highly appreciate your help. I am using standard SMD tutorial
>> code from
>> NAMD website. Any script contribution will be of great help.
>>
>> Thank you,
>>
>> S
>>
>>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> +1 (206) 714 4303
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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