AMBER Archive (2006)

Subject: RE: AMBER: periodic boundary condition question...

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Oct 30 2006 - 10:24:26 CST

Dear Hayden,

Just to add a note to what Sergey has suggested. To setup an arbitrary box I
tend to just edit the prmtop and inpcrd files. You can take any non-periodic
gas phase system and make it periodic as follows:

1) Edit the prmtop file and change integer number 28 under FLAG POINTERS
from a 0 to a 1. This corresponds to IFBOX and sets it to be a rectangular
box.

E.g.

%FLAG POINTERS
%FORMAT(10I8)
   12612 8 12586 27 50 37 68 56 0
0
   16999 4189 27 37 56 7 7 4 8
1
       0 0 0 0 0 0 0 1 50
0
       0 ------------------^^^
%FLAG ATOM_NAME

2) Edit the inpcrd file and go to the very end and add an extra line
specifying the box dimensions and angles. E.g.:

   0.2600185 -0.0278614 -0.3914518 -0.3403873 0.0352089 -0.0657586
  -0.7078672 -1.0816187 -0.8088763 0.7129222 0.3958158 -0.4476359
  54.9982251 51.7160934 44.9890188 90.0000000 90.0000000 90.0000000

Here my box is 54.998 A x 51.716 A x 44.989 A with all angles 90 degrees. A
rectangular box.

You can then run this as a periodic simulation. Just be aware that you
should not use constant pressure here or due to all the 'vacuum' space
things will break pretty quickly. constant volume simulations should be fine
though.

There may well be a better way to do this in Leap but I have always found
the above to work fine for me so that is what I stick with.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Sergey Samsonov
> Sent: Monday, October 30, 2006 07:36
> To: amber_at_scripps.edu
> Subject: Re: AMBER: periodic boundary condition question...
>
> Dear Mr. Eastwood,
>
> HL Eastwood wrote:
> > Sergey
> >
> > Thankyou for getting back to me. I have seen the setBox
> command, but I
> > don't get how it works. If you can indeed specify the box
> dimensions
> > then why are box dimensions not supplied as an argument? I
> would have
> > thought it would work something along the lines of: setBOX <unit>
> > <atomic atom name> <x coor> <y coor> <z coor>
> > My question is therefore:
> >
> > How using the "setbox" command can I set up a periodic box
> of 8 x 8 x 20?
> It is not as straightforward I suppose, unfortunately. The
> only thing to
> be specified is the distance between the atoms and the planes
> of the box
> (exactly this buffer), so I would suggest you to calculate
> the linear sizes
> of your molecule and then add (x_size_of_your_box - X_linear_size_of
> your_molecule)/2 as the X-buffer.
>
> I hope it would help.
>
> With best regards,
>
> Sergey
> >
> > many in thanks in advance
> >
> > Hayden Eastwood
> >
> >
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