AMBER Archive (2008)

Subject: RE: AMBER: Origin of periodic box

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Oct 15 2008 - 20:57:47 CDT

Hi Naser,

 

I believe that the origin is one corner of the box so for the initial
coordinates these should be between 0 and the xbox, ybox and zbox sizes.
Note though that during a simulation if you don't wrap then sander keeps the
coordinates of the original atoms and not their images ones so an atom could
for example move out one side of the box and then have negative coordinates
- I believe the origin should remain as the corner of the box though.

 

As for the zeroing of velocities I am not sure why ptraj does this but it is
a known issue and people have discussed it on the archive before. E.g.
http://archive.ambermd.org/200602/0222.html

 

Tom Cheatham may be able to expand some more on this. For the time being
your best option for imaging is to do a single step MD run with iwrap=1 to
get you a imaged restart file that will still have the velocities in.

 

All the best

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Naser Alijabbari
Sent: Wednesday, October 15, 2008 6:34 PM
To: amber_at_scripps.edu
Subject: AMBER: Origin of periodic box

 

Dear community,

Here is a sample of my coordinates from a restart file:

 11.3821583 18.1661542 24.1323434 12.0606145 18.8372653 26.0152123

  11.5071003 18.9571744 26.9465253 12.8878889 17.5565535 26.1569275

  13.4276408 17.4890159 25.2123598 13.6155085 17.6783609 26.9593194

 

This is my periodic box information:

solvatebox 2trx TIP3PBOX 8

  Solute vdw bounding box: 32.421 37.765 37.628

  Total bounding box for atom centers: 48.421 53.765 53.628

 

I was wondering what the origin (0,0,0 = x,y,z) is for the above coordinates
or how are the coordinates assigned for each atom (I am guessing it can't be
the center of my box because then my 26.5 would be my largest coordinate,
and I would also have negative coordinate values which I don't see.)

 

Also I tried using the below commands to create a new restart file:

trajin bbprotein5.rst

center :1-108

image center familiar

trajout bbproteincntrd.rst restart

 

I thought this would only affect my coordinates but looking at the new
restart file my velocities are all zeroed. Can someone explain why?

For example I might have the following velocity information:

 -0.1213716 0.2252365 -0.1331371 0.4267375 -1.6400259 -0.0792864

   0.1190042 0.5353082 -0.3345033 -0.5339086 0.1233047 0.5253997

  -0.0889908 0.0161328 0.1234542 -0.3570667 -0.6634506 0.0428914

 

and the new restart velocities would be as follows:

   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

 

Thanks

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