[gmx-users] Regarding trjconv

Erik Marklund erik.marklund at kemi.uu.se
Thu Nov 17 13:36:34 CET 2016

Dear Aparamita,

trjconv can enable or preclude subsequent analysis of trajectories, depending on what you want to do. For example, by fitting chosen groups to a reference structure. By centering your protein, you effectively remove all lateral diffusion, so it’s not surprising that a very low diffusion coefficient is reported for the processed trajectory.

Kind regards,

> On 17 Nov 2016, at 08:53, Apramita Chand <apramita.chand at gmail.com> wrote:
> 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?
> Regards
> Apramita
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