Re: SMD restrain point in NAMD

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Aug 04 2009 - 13:09:26 CDT

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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