[gmx-users] How to read .dat file

[Qing Lv]

The file rms.xvg contains only RMSD values against the reference PDB structure; what I need to know is the contents of RMSD matrix between 2 trajectories.


Qing


At 2017-06-15 15:17:08, "Dd H" <ddhecnu at gmail.com> wrote:
>I think this link should be helpful.
>http://manual.gromacs.org/programs/gmx-rms.html
>You can have a look at rms.xvg file, it contains rmsd values.
>
>Best regards,
>Dading Huang
>
>
>On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv <lvqingjiejie at 163.com> wrote:
>
>> I generated a .dat file with the following command:
>> gmx rms -s xxxx.pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm
>> -bin rms.dat
>> But how to read the binary file rms.dat?
>>
>>
>> The reason is that,
>> I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know
>> which frame in 1.xtc and which frame in 2.xtc have this minimal RMSD?
>>
>>
>> Thanks,
>> Qing
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