AMBER Archive (2009)

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

From: Jio M (
Date: Thu Aug 20 2009 - 23:43:31 CDT

Thanks Ross Walker and Bill Ross,

Thanks for quick nice advice and suggestions. Regarding concentrated I
meant just that, as number of total residues will remain same as before
((my sysytem has solute central + surrounding few organic molecules +
many  waters )).  if the volume is reduced, density will
increase and hence collisions ,that what I actually want, to increase
the possibilty of interaction of residues with central solute.

But at same time  I will consider your suggestions regarding Barostat while running MD.

Thanks and Regards


''''''''''''''''''''''''''''''''''  ''''''''''''''''''''''''''''

> 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.

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