[gmx-users] extracting a list of frames from a trajectory

[Irem Altan]

Hi,

I’m trying to extract a list of frames from a long trajectory:

gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc atom -o conf_test.gro -sep

where frames.ndx contains the following:

[ frames ]
2 3 4 5 6 8 ...

Each frame is supposed to be separated by 10 ps, so that for frame 2, t= 20.0000. Hence, conf_test1.gro starts with "Generated by trjconv : Protein in water t=  20.00000”, which is what we expect. However, the timestamps in the subsequent files are:

Generated by trjconv : Protein in water t=  30.00000
Generated by trjconv : Protein in water t=  40.00000
Generated by trjconv : Protein in water t=  50.00000
Generated by trjconv : Protein in water t=  70.00000
Generated by trjconv : Protein in water t=  80.00000
…

while it should have been 30, 40, 50, 60, 80, .... This happens a lot of times throughout the whole list of frames. Why does it happen? How can I fix it?

Best,
Irem