VMD-L Mailing List

From: Nuno Loureiro Ferreira (nunolf_at_ci.uc.pt)
Date: Fri Sep 28 2007 - 03:45:32 CDT

Hi Kutty

Please remember. Post your vmd related questions to the mailing list.
VMD community likes to help ;-)
Took the liberty to re-direct your e-mail.

M kutty wrote:
> Hello Nuno,
> The specific problem is this.
> I am monitoring the distance the directions of movement of an atom
> (say "protein and resid 34 and name CA") atom with another atom in
> resid 43. But after around 0.5 ns the 34:CA just flips around and
> interacts with another atom in residue (say 121). Again the residue
> flips back and interacts with resid 44. So I want to highlight the
> interacting atoms at a specific time point with a VDW representation.
>
> I have a data file which is like this :
>
> TimeStep(ps) Residue and Atom Residue and Atom
> ----------------------------------------------------------------------------------
> .
> .
> .
>
> 101 34 : CA
> 45 : CB
> 102 34 : CA
> 46 : CG
> .
> .
> .
> .
>
> Which means that at 101ps 34:CA interacts with 45 : CB and so on.
>
> How can this be done ?
>
I never done that, but ...
Check Axel's excellent cpmd-vmd manual at
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/index.html
 Read the dynamic atom selection chapter (chap 6), it could give you
some answers.
Cheers,
Nuno
>
> Thank you,
> Kutty
>
>
>
> > Date: Wed, 19 Sep 2007 11:05:01 +0100
> > From: nunolf_at_ci.uc.pt
> > To: mkutty_lists_at_hotmail.com; vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: Residue highlighting in MD Traj
> >
> > Hi Kutty
> >
> > M kutty wrote:
> > > Hello,
> > > I am analyzing an MD traj. I have to monitor a set of residue up till
> > > a certain time point (say 500ps) and then monitor another set upto
> > > another time point.
> > > How would I go about doing it ?
> > >
> >
> > This is to vague to give you an oriented answer. But obviously the
> > answer is, use a different atom selection.
> > Can you give us a minimal example of what you are doing?
> > Cheers,
> > Nuno
> >
> >
> > >
> > >
> > >
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