From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Nov 26 2007 - 14:03:38 CST
could you verify that you are
-starting your simulation at timestep 0
-verify that the coordinates in your smdfile are identical to those
present in the first timestep?
These are the two most obvious causes I can think of for a high initial
Vamshi Gangupomu wrote:
> 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 suggestions.
> On 11/26/07, *Carsten Olbrich* <ocarsten_at_googlemail.com
> <mailto:ocarsten_at_googlemail.com>> 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.
> On Nov 25, 2007 7:33 AM, Vamshi Gangupomu < krish833_at_gmail.com
> <mailto:krish833_at_gmail.com>> 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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