AMBER Archive (2009)

Subject: RE: [AMBER] box volume not understood?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 20 2009 - 18:21:00 CDT

Hi Jiomm,

> Actually I want to reduce the box volume ,after solvation, by using set
> Unit box {  } command to make my system more concentrated. That
> made me confused which dimension I should play with.

The easiest way to do this, if you really just want to reduce the box size
is to write out a prmtop and inpcrd file. Then edit the inpcrd file and look
at the last line. This gives the box dimensions A,B,C and the angles. You
can then modify these values as you see fit.

> >cube is 27.40838^3 = 20589.704 A^3
>
> as above clears that 27.40838 is dimension of cube, so in set command
> if I use dimensions like set Unit {22 22 22} that is values less than
> 27.40838 will make my cube small. but will it ensure that truncated
> octahedron which was fitting in 27.40838 dimensioned cube box will
> adjust itself to get fit into {22 22 22} cube box so that my solvated
> system get concentrated

I'm not sure I understand what you mean by more concentrated. Note you can
set the box size to anything you want. Be aware though that just setting the
box smaller will not do anything to the coordinates. You will just get
massive VDW forces due to atoms sitting on top of each other at the
beginning and your system will probably explode.

If you mean that you want the water to be denser for your system then you
should think carefully about what you really want to do. Note water is
EXTREMELY incompressible. If I remember correctly water is about 10,000
times less compressible than steel. Hence it will take an extreme amount of
pressure to increase your water box density, if this is what you want to do?

You could always run in sander/pmemd with the barostat turned on an a high
pressure target set. Note though that you are really moving out of the realm
that the water model was designed for. Also note that if you do artificially
make your system denser as soon as you run NPT it is going to adjust back to
the target pressure. Thus at 1 atm you will always tend to approx 1g/cm^3.
The same is true for the initial xleap built structure. Note the density
isn't really 0.73g/cm3. It is just that the box has been made artificially
big to avoid initial problems when starting MD.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber