Subject: CHARMM Crystal problems...

From: Joshua Speidel <[email-masked]>
Date: Thu, 23 May 2002 16:02:15 -0400

Hello,

I am trying to set up a PME molecular dynamics system, and have been having
trouble getting past the crystal build command. I'm trying to use a
hexagonal box.  After I've read in coordinates, topology etc., I use these
commands to build the crystal:

CRYSTAL DEFINE HEXA 72.0 72.0 27.0 90.0 90.0 120.0
CRYSTAL BUILD CUTOFF 12.5 NOPER 5
(-Y,X-Y,Z)
(-X+Y,-X,Z)
(-X,-Y,Z)
(Y,-X+Y,Z)
(X-Y,X,Z)

OPEN WRITE UNIT 9 CARD NAME "./hexa12.5.xtl"
CRYSTAL WRITE UNIT 9 CARD

... This part appears to work fine, but should I be concerned about the
message 'THERE ARE ROTATIONS FOR THIS TRANSFORMATION SET' that I get at the
end of the transformations? How do I / Should I include these when I go on
> from here? Also, the operations that I included are for a P6 hexagonal
prism, but I saw in the test files provided with charmm that when they test
the different kinds of crystals they don't use operations.  Should I be
using them?

In my next step, I simply try to calculate the energy.  Using the same input
file I deleted last two lines 'OPEN WRITE ...' and 'CRYSTAL WRITE ...' and
added a line that simply says 'ENERGY'

In the output, it starts

 CHARMM>    energy

 <MKIMAT>: updating the image atom lists and remapping

...and then it says
***** LEVEL -3 WARNING FROM <MKIMAT> *****
***** RESIDUE NUMBER OVERFLOW

even though my sysem has only 3200 residues and 11000 atoms.  I'm not sure
what is happening.

I feel that the inability to calculate the energy is related to my questions
about the crystal, but I'm not sure.  Comments on any part of this long
email are greatly appreciated.

Thank you,

Josh

ps. This is less critical, so I put it at the end, but while trying to make
the hexa.xlt file, I found that CUTOFF 15 and CUTOFF 16 caused the program
to crash, but that a CUTOFF of 12.5, 14.5, and 20 worked okay (as far as I
could tell).  I'm really curious as to why this is.  Any thoughts? Thanks!

---
Joshua Speidel
Graduate Student
Mount Sinai School of Medicine
New York, NY 10029