[gmx-users] g_mindist after trjconv -fit give different results

eladp at post.tau.ac.il eladp at post.tau.ac.il
Sun Dec 6 20:50:30 CET 2009

Hi Tsjerk,
thanks for the reply.

Will the MSD of the molecule also be affected by the fitting.
I'm trying to calculate the relative diffusion coefficient of an ion  
near a protein. For this I thought to first fix the system according  
to the protein and then calculate the msd of the ion.
I noticed in the g_msd code that periodicity is taken into account (as  
expected). However, in g_msd the interest of the periodicity handling  
regards regards the atom position relative to itself in previous  
frames. Will this relative movement (of the atom in relation to itself  
in the previous frame) be kept after doing "trjconv -fit".


> Hi Elad,
> This has been mentioned several times before, in a different context.
> But fitting only affects coordinates, and not the PBC. So after
> fitting the coordinates and the PBC don't match any more and any
> analysis requiring PBC, such as calculating minimal distances, will
> give garbled results. Always do such things on untransformed
> trajectories.
> Cheers,
> Tsjerk
> On Fri, Dec 4, 2009 at 7:43 PM,  <eladp at post.tau.ac.il> wrote:
>> Hi all,
>> I have a system of protein+water+ions.
>> I measured the minimum distance between one of the ions to the protein.
>> Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
>> Did the same mindist again and the graphs are not always identical.
>> Any suggestions?
>> I use gromacs 4.0.5 with an octahedron box.
>> same problem happens when I do trjconv -fit rot but does not happen when
>> -fit trans.
>> In VMD I do see a difference in the position of the ion relative to the
>> protein.
>> Thanks.
>> Elad P.

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