[gmx-users] How to calculate the spatial distribution function for the last 50ns of the trajectory?

[Peiyin Lee]

Hi, Christian,

   Thank you for your reply. I'm using Gromacs 2018 and I've tried to
output .xtc files instead of .tng files and it worked! It seems that the
issue is really related to the way Gromacs outputs .tng file. Thank you for
the help!

Regards,
Peiyin

On Thu, Dec 5, 2019 at 4:29 AM Christian Blau <blau at kth.se> wrote:

> Hi Peiyin,
>
>
> There is a related redmine entry that suggests this might be fixed in
> newer versions of GROMACS
> https://redmine.gromacs.org/issues/2189
>
> (from GROMACS2018 on). If you are using a newer GROMACS version, to rule
> out that this is an issue related to .tng, can
> you try using the older .xtc format instead?
>
>
> Best,
> Chrstian
>
> On 2019-12-05 03:13, Peiyin Lee wrote:
> > Dear users,
> >
> >     I have a simulation that has a 400 ns trajectory and I would like to
> > calculate the spatial distribution function of the last 50ns. I followed
> > the instructions on gmx_spatial manual and everything was ok if I run the
> > first 50ns of the trajectory instead of the last 50 ns. However, once I
> > changed the command from gmx_mpi trjconv -s md.tpr -f md.xtc -b 0 -e
> 50000
> > -o b.tng -boxcenter tric -ur compact -pbc none
> > to gmx_mpi trjconv -s md.tpr -f md.xtc -b 350000 -e 400000 -o b.tng
> > -boxcenter tric -ur compact -pbc none
> > and then ran gmx_mpi trjconv -s md.tpr -f b.tng  -o c.tng -fit rot+trans
> > I would get an error saying:
> >
> > WARNING: Incomplete frame: nr 0 time 0
> >
> >
> > WARNING no output, last frame read at t=0
> >
> > I have checked my trajectory with gmx_check and the trajectory is fine. I
> > wonder why those two commands only work with -b 0, but not -b
> anyothertime.
> > Does anyone have an idea? Thank you in advance!
> >
> > Regards,
> > Peiyin
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