[gmx-users] RE: micelles and trjconv -pbc cluster

[Ran Friedman]

Hi,

Likewise, I have a modified version of g_clustsize that calculates the radius of gyration for the largest structure and can send you the code. 

Ran
------------------------------------------------
Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.friedman at lnu.se
http://lnu.se/ccbg
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Message: 4
Date: Thu, 14 Apr 2011 17:44:07 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] micelles and trjconv -pbc cluster
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <BANLkTin-YV43F=s1r-NG8XNZJ9EJEqrXew at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi George,

Recently I wrote an alternative, non-iterative clustering routine, that does
not suffer from convergence failures. If you want, I can send you the
modified trjconv source code. Note that it does not bother about the center
of mass of the cluster, but just builds a network of neighbours, until there
are no more. If you're clusters are not periodic, it won't matter.

Let me know...

Cheers,

Tsjerk

On Thu, Apr 14, 2011 at 4:48 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

>  jim jack skrev 2011-04-14 16.42:
>
>   Dear GROMACS users,
>
>    I am trying to simulate an SDS micelle in water. As simulation time goes
> by, the micelle approaches the edge of the box and consequently some of
> these molecules get in from the other side. This leads to incorrect radius
> of gyration, eccentricity, etc. A solution to this problem is the option trjconv
> -pbc cluster as described in the page
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering. In this
> case, the problem is that it takes a lot of time and a huge file (several
> GB) is created due to this procedure. Is there any other alternative?
>
> Thanks in advance
>
> George Koros
>
>    I don't think that the cluster option always converges. You could, if
> your micelle is intact at frame 0, first do trjconv -pbc nojump, then
> optionally trjconv -center. That should give a trajectory from which you
> could calculate the radius of gyration. If SDS molecules occationally leave
> the micelle and recombine with a priodic, then you might have a problem with
> the suggested approach.
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
>
> --
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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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