AMBER Archive (2005)

Subject: RE: AMBER: Increasing Volume with ntb=1

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 27 2005 - 12:13:27 CST

Dear Harianto,

 what I see is something strange: protein often comes in and
> out of the
> water box. Is it because of the periodic box? But the fact
> that part of
> protein is outside and the rest is inside, will that mess the
> calculation?

I took a look at your output file and everything looks fine. The issue you
discuss with the protein sticking out of the box is an issue with
visualisation rather than with the periodic boundaries. If you were NOT
running periodic boundaries then the condition you describe would be very
worrying. In the periodic boundary case it is simply an issue of what has
been chosen for the origin when you reimaged the mdcrd file. Wrapping of
coordinates is done on a residue basis (or possibly molecule basis, have to
check) and as such the atoms that move outside of the box will not have
their positions wrapped until the whole residue has moved out of the box.
This doesn't effect the calculation as it handles this situation. However,
when visualising a system it can look very strange. However, it is better
than wrapping each atom at a time since then you would get massive jumps in
an RMSD calculation as an atom crossed the box boundary. You would also get
exceedingly long bonds being drawn by programs like VMD which don't know
about the periodic nature of the system.

Your best option, if you want an easier to visualise simulation is to
reimage the MDCRD but centred on your molecules of interest. Pick a residue
in the middle of your molecule. This will then be chosen as the origin and
so should when visualised appear to remain in the centre of the box. See the
ptraj section of the manual for details on the center keyword.

> Btw, I noticed that your opinion about the summary.VOLUME file is
> correct, it just has 1 column (time series), so no volume
> info in it. I
> dont know why there is no volume reported in the output file.

The volume is not written to the output file since it is constant during the
run. The software actually fixes the volume of the box and consequently the
volume cannot vary unless there is some strange bug. Hence there is nothing
to be gained from writing it to the output file.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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