[gmx-users] Regarding trjconv

Apramita Chand apramita.chand at gmail.com
Thu Nov 17 08:53:23 CET 2016

Dear All,
I had one doubt regarding g_trjconv which I used to center my protein after
simulation. I got different diffusion values when I used the .xtc file
before and after applying trjconv. Which one should be used?  Is trjconv
just for visualisation or is necessary for analysis too? Does it change the
values or interactions in any way?
For example, the diffusion values that I got were
                  Before trjconv           After Trjconv
Urea -          1.6628                      2.089
Protein  -        0.0927                    0.000108
Water               2.513                      2.59

Please advise. Which values should be taken?


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