[gmx-users] Subtract structure to a trajectory

[Marco Gerolin]

Hello James,
actually I don't need to calculate the RMSF, i need the subtracted
trajectory to calculate some correlation functions.
It seems to me that the unique solution is to write a TCL script ad hoc.
I'm totally new with TCL , so probably it would take some time, but it's
not a problem.

Thank you for helping!


2014-07-11 8:56 GMT+02:00 James <jamesresearching at gmail.com>:

> Dear Marco,
>
> If no-one can suggest a Gromacs tool, it would be easy to output all the
> co-ordinates of the atoms and then calculate (atom position) - (average
> structure position) during post-processing. But maybe you know this
> already.
>
> James
>
>
> On 10 July 2014 22:59, Marco Gerolin <marco.gerolin at studenti.unipd.it>
> wrote:
>
> > Dear Gromacs users,
> >
> > I have an MD trajectory, and I need to subtract for each atom and each
> > frame, the coordinate of an average structure.
> > Has Gromacs a tool capable of this?
> >
> >
> > Thank you
> > --
> > Marco Gerolin
> > Dipartimento di Scienze Chimiche
> > Università degli Studi di Padova
> > Via Marzolo 1, 35131
> > Padova
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-- 
Marco Gerolin
Dipartimento di Scienze Chimiche
Università degli Studi di Padova
Via Marzolo 1, 35131
Padova