Query regarding trajectory conversion from netcdf to xtc

User discussions
1

GROMACS version:
GROMACS modification: Yes/No

Hello,
I am converting amber trajectory which is in NETCDF format in XTC format with the help of mdconvert with command :
mdconvert gamd.m.nc -o gamd.xtc

But it shows me following error:
xdrfile error) Internal overflow compressing coordinates.
(xdrfile error) Internal overflow compressing coordinates.
(xdrfile error) Internal overflow compressing coordinates.
(xdrfile error) Internal overflow compressing coordinates.
(xdrfile error) Internal overflow compressing coordinates.
…

Why this error is occurring? Please assist .

Regards,
Munazzah Ansari

2

This question is not really GROMACS related, so you might get better support if you ask mdconvert experts/developers instead.

Have you checked that the netcdf file is correct? I presume there are tools for dumping its contents. Does it work if you convert it to another format, e.g., trr?

3

Thanks MagnusL, I think I have a problem with the trajectory file because on converting it to any format, it shows an error.