Re: interactions in flexible cel

From: Anna Modzelewska (
Date: Wed Jun 29 2005 - 02:07:04 CDT

Hi Swarna
I think this is a script for SMD in a flexible cell. It doesn't read the cell dimensions from a .xst file, does it?

I already finished my simulation and now I would like to calculate the energy of interaction for two proteins in my system. I found a script that calculates it basing on a .dcd file. The problem is, that in my case cell dimensions are different for each frame and I don't know how to input this information to the .conf file.

Maybe I just don't understand your script, if this is the case, could you please explain me how it works?

Best Regards
  ----- Original Message -----
  From: Swarna Patra
  To: Anna Modzelewska
  Sent: Wednesday, June 29, 2005 8:32 AM
  Subject: Re: namd-l: interactions in flexible cel

  Hi Ann,
  I have attached a file pl have a look..
  good luck
  On Wednesday 29 June 2005 15:34, Anna Modzelewska wrote:
> Hi,
> how to calculate energy of interaction for a simulation with constant
> pressure and flexible cell? I guess, I should add to the .conf file a
> script which would inform namd, that cell dimensions change every step.
> Does anyone have a such script?
> Thanks for help
> Anna
> ************************************************************************
> Anna Modzelewska, M.Sc.
> International Institute of Molecular and Cell Biology
> Trojdena 4, 02-109 Warsaw, Poland
> phone: +48 22 5970721 fax: +48 22 5970715
> ************************************************************************


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