AMBER Archive (2008)

Subject: RE: AMBER: How to manually adjust periodic boundary conditions (PBC)

From: Chin, Keith B (keith.b.chin_at_jpl.nasa.gov)
Date: Wed Nov 19 2008 - 19:15:17 CST

David:

OK, thanks.

Now, suppose I did create a supercell with good box dimensions, but the atom coordinates came from my own program (Not xleap).

How do I manually set periodic boundary conditions to hexagonal crystal lattice with alpha = 90, beta = 90, gamma = 120 (NOT box with alpha = 90, beta = 90, gamma = 90) to run MD in sander? I used the setbox command to set initial PBC close to actual lattice dimensions prior to changing it in last line of *crd (coordinate) file.

What about the *top (topography) file BOX_DIMENSION parameter such as:

%FLAG BOX_DIMENSIONS

%FORMAT(5E16.8)

  9.00000000E+01 1.15728620E+01 1.17719310E+01 1.31228620E+01

How does sander use these parameters as oppose to PBC dimensions in last line of *.crd file

Does sander recognize my atom coordinates as opposed to the ones created by xleap SaveamberParm in applying the my hex lattice parameters?

Any info would be greatly appreciated.

Thanks again in advance

-keith

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of David A. Case
Sent: Wednesday, November 19, 2008 3:36 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: How to manually adjust periodic boundary conditions (PBC)

On Wed, Nov 19, 2008, Chin, Keith B wrote:

>

> Suppose rather than a box lattice, I wish to apply PBC for hex lattice,

> where a=4.516, b= 4.516, c = 7.435, alpha = 90, beta = 90, gamma = 120.

Amber cannot do this small a unit cell. Basically, the box size must be at

least twice the cutoff + "skin" (usually 1 to 2 Ang.) Your only real

alternative is to simulate several unit cells as one "supercell". A cell size

of 18 Ang. is about the practical minimum for Amber.

>

> Ewald PARAMETER RANGE CHECKING:

> parameter skinnb+cutoffnb: (nonbond list cut) has value 0.12000E+02

> This is outside the legal range

> Lower limit: 0.00000E+00 Upper limit: 0.58665E+01

> Check ew_legal.h

This is basically saying (in jargon) what I said above. It looks like you are

setting the cutoff to 10, which is too large -- you should probably stick to

the default of 8.

...good luck...dac

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber_at_scripps.edu

To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

      to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu