Re: SMD Constant Velocity: Force

From: Vamshi Gangupomu (
Date: Mon Nov 26 2007 - 09:33:51 CST


I am not using a tcl-force script. I give my SMD paramaeters in the conf
file and use a reference file for the atoms to be pulled. I am not trying to
stretch or break open the nanotubes but just trying to move them in water.
So, my SMD atoms are the nanotube atoms and there are no fixed atoms. Let me
know if you see and red flags with the technique. Thanks a lot for your


On 11/26/07, Carsten Olbrich <> wrote:
> Hi Vamshi,
> Do you use a tcl-force script?
> If so then you have to ensure that the reference 'center of mass'
> (start position of the virtual spring) you use in the script is
> identical to that one of your selected atoms.
> Carsten
> On Nov 25, 2007 7:33 AM, Vamshi Gangupomu <> wrote:
> > Hello VMD Users,
> >
> > I am trying to use SMD to pull a nanotube using constant velocity
> pulling.
> > However, my initial force is very high. I was expecting the force to
> start a
> > zero and increase gradually, as shown in the protein pulling example.
> Any
> > inputs regarding how to solve this problem will be greatly appreciated.
> I am
> > not sure if some thing is wrong with my SMD technique.
> >
> >
> > Thanks,
> > Vamshi

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