[gmx-users] my own routine

Isabella Daidone i.daidone at caspur.it
Tue Apr 20 15:24:01 CEST 2004

> This all seems very strange.
> I have never heard of some frames being wrong and later frames being ok.
> The problem can only be in the xtc if some coordinates are really wrong,
> such as all coordinates being identical.
> You should be able to see this with ngmx.
> But then the gro files can not be ok.
> But how did you obtain the gro files then?
> I assume with trjconv, but with which options?

yes, I used trjconv. The trajectory I'm using has been centered and the
pbc has been removed. The .gro files are obtained with trjconv on this
trajectory without any extra options, i.e. just using the options -f -s
and -dump.

> Does the system you analyze consist of multiple molecules?

Yes, I have 26 peptides.
Do you have any idea?

> BTW There is a routine in gmxlib/princ.c called principal_comp that 
> calculates
> the geometrical axes, not using ql77, but using jacobi.

I'll check this.

> Berk.

Thank you

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