From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Dec 02 2013 - 01:43:41 CST
Hi Jim,
Thanks for your interest, I noticed that it seems to be related to loading
dcd files without box info. So namd uses of course the box it had before and
even small differences seem to break the coords here when namd starts to
depart the atoms to the patches again, or so. So this seems to be my error,
sorry for that. Nonetheless I would be nice to have a command loading or
setting the box information within TCL for the future.
Thank you for your interest.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: Jim Phillips [mailto:jim_at_ks.uiuc.edu]
> Gesendet: Samstag, 30. November 2013 21:35
> An: Norman Geist
> Betreff: Re: BUG: TCL coorfile command
>
>
> This appears to work for me. Can you send the full input files,
> especially the script for loading the dcd frames?
>
> Jim
>
>
> On Thu, 28 Nov 2013, Norman Geist wrote:
>
> > Dear developers,
> >
> >
> >
> > I observed the following behavior while using the coorfile command
> from the
> > TCL interface. If one loads a frame from a dcd, the coordinates seem
> to be
> > distorted somehow what causes high energies when continuing the
> simulation
> > with the loaded coordinates also if a minimization follows. One can
> easily
> > see the problem if one uses "output" to write a .coor right after
> having
> > loaded the frame, and compares it to the original coordinates in vmd.
> One
> > can see that parts/slices of the molecule seem to be displaces in a
> whole.
> > This is really a problem for me as it is impossible to continue the
> > simulation due extremely high forces which the minimize can't
> resolve.
> >
> >
> >
> > If there is another option to load new coordinates into the
> simulation, I'd
> > appreciate to know.
> >
> >
> >
> > I'll append my structure that show what is happening. The evo coor is
> the
> > original. A dcd is generated from it. This dcd and the evo.coor are
> exactly
> > equal. The test.coor is written due "output" right after "coorfile
> read".
> >
> >
> >
> > Please conform.
> >
> >
> >
> > Thanks
> >
> >
> >
> > Norman Geist
> >
> >
> >
> > ---
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> >
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