Re: Techinal problems with ABF simulations

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jun 27 2012 - 08:29:09 CDT

Dear Artturi,

With the collective variables module in recent versions of NAMD, here
is how you would proceed:

1) define all reaction coordinates separately ('colvar' blocks)
2) define several separate ABF biases ('abf' blocks), each one
accessing the relevant colvar.

Best,
Jérôme

On 27 June 2012 14:44, Koivuniemi Artturi <Artturi.Koivuniemi_at_vtt.fi> wrote:
> Dear Jenin,
>
>
>
> I’am researcher in VTT Technical Research Center of Finland and I would like
> to ask help from you concerning the technical details of adaptive biasing
> force simulations. I’am planning to conduct ABF simulations with NAMD
> software and I would like to ask how did you setup ABF simulations for
> aqauglyceroporin with four glycerols that was described in the paper: Henin
> et al. Diffusion of Glycerol through Escherichia coli Aquaglyceroporin GlpF,
> Biophysical Journal, 2008.  I’am able to run AFB with one glycerol, but I
> have not managed to do it with four glycerols as was described in the paper.
> In particular, I’m interested how the following thing is handled in NAMD: To
> enhance the statistical information supplied by the simulations, the
> assisted transport of glycerol was investigated along that spatial
> direction, in the four channels of GlpF, through the definition of four
> independent reaction coordinates. So I’m not able to define four different
> reaction coordinates and output files to run a similar simulations. I would
> pleased if you have time to lighten up the protocol for me.
>
>
>
> Best regards,
>
> Artturi Koivuniemi
>
>
>
>
>
>
>
>
>
> www: www.vtt.fi/research/area/biotechnology_health_well_being.jsp?lang=en
>
> YouTube: www.youtube.com/user/VTTFinland
>
>
>
> ---------------------------------------------------------------
>
> Artturi Koivuniemi
>
> Researcher
>
> Biotechnology for Health and Well-being
>
> VTT Technical Research Centre of Finland
>
> Tietotie 2, Espoo, P.O.Box 1000, FI-02044-VTT
>
> Tel: +558 20277 4472
>
>

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