[gmx-users] micelle clustering

[Tsjerk Wassenaar]

Hi Sulatha,

Did you install gromacs yourself or are you using a system wide
installation?

A. I installed myself

In that case you go into the directory where you have put the gromacs source
code and put the modified version of gmx_trjconv.c in the subdirectory
src/tools. Then you go into that directory and type 'make trjconv'

B. I just used what was available already

If you're good friends with the system administrator you can ask him/her to
compile the modified trjconv, as under A.
Otherwise, you'd better install gromacs yourself as explained on the gromacs
site and then go to A.

Hope it helps,

Tsjerk

On Thu, Jun 30, 2011 at 10:10 AM, gregory megariotis
<gmegariotis at yahoo.gr>wrote:

> Dear Sulatha,
>
> You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002with GROMACS 4.5.4.
>
> Best regrds
>
> Grigoris
>
> --- Στις *Πέμ., 30/06/11, ο/η sulatha M. S <mssulatha at gmail.com>* έγραψε:
>
>
> Από: sulatha M. S <mssulatha at gmail.com>
> Θέμα: [gmx-users] micelle clustering
> Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18
>
>
> Hi all,
>
> I have simulated a system of randomly dispersed surfactants in water using
> gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns.
>  I am using a time step of 0.002 fs with xtc files written every 500
> steps. For analyzing the micellar properties, I tried the commands given in
>
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering
>
> and also looked at the various posts given on this topic, (specifically
> Chris Neale's and Tsjerk's mails).
>
> As posted by Chris Neale, I tried using the commands,
>
> 1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just
>
> get one frame)
>
> 2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr
>
> 3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump
>
>
>
> Also mentioned in Tsjerk' post that
>
> "When doing so, be sure to use a frame which is close enough to the
>
> starting frame in terms of the coordinates. -pbc nojump works based on
>
> the coordinates and if you use a reference which doesn't match the
>
> starting frame close enough everything can get really messed up".
>
>
>
>
>
> I tried the command 1 with
>
>  trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002
>
> and also
>
>  trjconv -f a.xtc -o b.gro -pbc cluster -dump X (where x=2, 4, 6, 8 etc..)
>
> The program gets into a never ending loop.
>
> I also tried the command 1 on a later part of the trajectory (after 40 ns),
> there also the program enters in a indefinite loop.
>
> I will greatly appreciate any help on how to go about doing this
> specifically which frame (for dump or -e argument) .  Please guide me on
> this.
>
> I also downloaded the modified trjconv.c  by Tsjerk (in one of his posts
> on micelle clustering), but do not know where to incorporate this. I need
> some help on how to use this modified trjconv code.
>
>
> Thanks for any help or clue,
>
> Sulatha
>
>
>
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>
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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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