[gmx-users] Regarding trjconv
erik.marklund at kemi.uu.se
Thu Nov 17 13:36:34 CET 2016
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.
> 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?
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