From: Do Nhu Trang (dntrang_at_gmail.com)
Date: Fri Jan 09 2009 - 10:17:02 CST
Many thanks to Axel.
I'm new to NAMD and also VMD, so I don't know much about these tools. I'm
trying to follow your suggestion.
Bests,
Trang.
On 1/9/09, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> On Fri, 9 Jan 2009, Do Nhu Trang wrote:
>
> DNT> Thanks so much for the suggestions.
> DNT> The protocol of Joshua works well with the constraints on whole system
> with
> DNT> the same force and the constraints decrease uniformly as he said. But
> my
> DNT> case is a little bit different. I need to apply the constraints to a
> part of
> DNT> the system and the time of different constraints are different.
> DNT> So now, the easiest way I found is splitting the simulation into
> stages.
>
> DNT> However, by doing so, I have problem in watching the whole evolution
> of the
> DNT> trajectories.
>
> why so?? you can easily load multiple trajectory files "on top of each
> other" into visualization tools like VMD. not to mention the fact that
> with the catdcd tool (bundled with VMD) you can also concatenate
> multiple dcd files into one (although in most cases it is convenient
> to keep them apart).
>
> cheers,
> axel.
>
> DNT> I still need a more graceful and efficient way. Any more suggestion?
> DNT>
> DNT> Bests,
> DNT> Trang.
>
> DNT>
> DNT>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
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