Re: help

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Apr 22 2010 - 16:44:58 CDT

Dear Guodong,

I am copying this message to the NAMD mailing list in case the
discussion could help other users.

The type of calculation reported in that paper can be performed using
4 independent ABF biases, each acting on one collective variable. So
the colvars config file would (roughly) look like:

colvar {
  name zA
  (...)
  distanceZ {
   (...)
   }
}
colvar {
  name zB
  (...)
  distanceZ {
   (...)
   }
}
colvar {
  name zC
  (...)
  distanceZ {
   (...)
   }
}
colvar {
  name zD
  (...)
  distanceZ {
   (...)
   }
}

abf {
  colvars zA
}
abf {
  colvars zB
}
abf {
  colvars zC
}
abf {
  colvars zD
}

Best,
Jerome

On 22 April 2010 22:18, Guodong Hu <guodong.hu537_at_gmail.com> wrote:
>
> Dear jerome
>
> I have studied the paper "Diffusion of glycerol through Escherichia coli
> aquaglyceroporin Glpf". I'm going to do similar work use ABF method. In your
> paper, the glycerol throgh Glpf with four channels and every channel do the
> ABF calculation. I use the NAMD2.7. After read the ug of namd and the
> tutorial of ABF. I still unknow how to write the files. All my efforts was
> lost. Can you give me some advices? If you give me a example, that would
> be very good. Thank you
>
> Guodong Hu
> 2010-04-22
> ________________________________
> Guodong Hu

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