I've having some problems with use of the option '-fitall'.
The command I'm using is:
g_rms -hidden -fitall -s ../topol_amber.tpr -f ../amber99sb_skip10.xtc -f2
../amber99sb_skip10.xtc -m rmsd.xpm
But a diff with the rmsd.xpm file I got without using '-fitall' reveals
that the files are identical
Yes, thanks. My first impulse was to do a python script to do the
conversion, but Tsjerk Wassenaar's script works neat :)
On Mon, Jan 23, 2012 at 5:10 PM, lina wrote:
> On Mon, Jan 23, 2012 at 9:56 PM, Víctor
> wrote:
> > Dear all,
> >
> > I've been trying to do a rmsd matrix of two different
On Mon, Jan 23, 2012 at 9:56 PM, Víctor wrote:
> Dear all,
>
> I've been trying to do a rmsd matrix of two different trajectories by using
> g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms
> uses does something like this:
>
> for each frame f1 in traj1:
> for each fram
Thanks a lot, your answer has been very useful!
Btw, do you know why is the default matrix used more often than the other?
(I see that It's faster, but maybe there's another reason)
On Mon, Jan 23, 2012 at 3:39 PM, Tsjerk Wassenaar wrote:
> Hi Victor,
>
> By default it does this:
>
> > for each
Hi Victor,
By default it does this:
> for each frame f in traj1:
> superimpose f with first frame
>
> for each frame f1 in traj1:
> for each frame f2 in traj2:
> calculateRMSD f1, f2
But there's a hidden option -fitall that gives you the other. Check
g_rms -h -hidden
> I've also been t
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