[gmx-users] gmx trjconv

[Dallas Warren]

This might be a better group of commands:

3 / gmx trjconv -f a.xtc -o a_cluster_center.xtc  -pbc cluster -center
..... select the micelle constructing molecules to cluster and center on,
then System or Non-Water as the output
4 / gmx trjconv -f a_cluster_center.xtc - a_whole.xtc -pbc mol

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 17 Jan 2020 at 04:53, Giuseppe R Del Sorbo <del-sorbo at ill.fr> wrote:

> Dear users,
>
> I might need an help with gmx trjconv.
>
>
> I have a system with a lysine + a micelle attached on it and I have to
> analyse the radial spherical distribution on the micelle.
>
> The idea is to center the micelle and to work on it.
>
> I used the command "gmx trjconv - cluster" to get a centered micelle and
> if I visualize it in vmd everything is fine.
>
> Accordind with the manual I have to follow this three steps:
>
>
>      1) trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
>      2) grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
>      3) trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
>
> For the first two steps everything is ok, but for the last one it
> doesnt't work. Gromacs doesn't give any error, but it doesn't run.
>
> Than I tried to write the third step without "-pbc nojump" and it works,
> but the trajectory is a mess and I can also see the lysine, when I
> should only see the micelle..
>
> Do you have any suggestion?
>
> Thanks a lot
>
>
> Giuseppe
>
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