Re: Issues with SMD

From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Mon May 10 2004 - 23:53:13 CDT

Hi,
The position of the virtual particle, which is attached to the real atoms
via a spring, is calculated by multiplying the timestep by the SMD
velocity. Increasing the firsttimestep changes the position of the
virtual particle at the beginning of the run and stretches the spring
out, yielding a higher force. What's important to note is that if you are
continuing a run, you need to make sure that the firsttimestep value is
continued from the previous run. (If you choose 0, your virtual particle
will move back to its original position and the protein will be pulled
backwards.)
There is at least one piece of code in the mailing list archives to grab
the firsttimestep from your previous runs. It just so happens to be
written by Gadi. **cue eerie music**

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0677.html

Tim

On Mon, 10 May 2004, Brian Bennion wrote:

> Hello,
>
>
> Has anything been done to address the problem below? If so it would be
> nice to post a followup message...
>
>
> Regards,
> Brian
>
> On Mon, 26 Apr 2004, Gadi Oron wrote:
>
> > Hi,
> >
> > I have found an issue with SMD. When SMD is used, and the starting
> > timestep is not 0, the SMD force is calculated wrongly.
> >
> > Compare:
> >
> > FirstTimeStep = 160000
> > SMD 160000 -1.00756 -0.140782 29.1221 0 0 5618.41
> >
> > FirstTimeStep = 0
> > SMD 0 -1.00756 -0.140782 29.1221 0 0 849.376
> >
> > A bug?
> >
> > Regards
> > --
> > ================= Gadi ORON, PhD -o- Proteologics ======================
> > ========== gadi/at/proteologics.com ========== +972 8 9475666 ==========
> > Most burning issues generate far more heat than light.
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> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
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