Re: CCL:protein cross the boundary of the box in PBC

	First, I'd like to suggest using the CHARMM discussion Forums at
 www.charmm.org; people from several of the development groups regularly
 read and answer posts, and the message threads are searchable.
 N.B.  CHARMM == academic, CHARMm == commercial
 	There's an arcane feature known as image patching (IMPATCH; see
 images.doc) which allows creating a bond to an image molecule;
 historically, I believe DNA simulations were attempted using this.
 There are a number of restrictions and requirements:
 [1] IMAGE facility only, not CRYSTal
 [2] must create the image patch
 [3] must account for ANGLE, DIHEDRAL terms in the patch
 [4] must prepare image transformation list
 [5] cannot use Ewald or CPT methods (both require CRYSTal)
 On Tue, 22 Jun 2004, Wei Shi wrote:
 > I am planning to do MD simulations for a pretty large system. The
 > system is composed of several protein molecules. I want to apply
 > periodic boundary condition in the Z direction for the system.
 > However, one of the protein will cross the boundary of the PBC box I
 > am going to use. How does the CHARMm (academic cersion) deal with this
 > kind of probelm? Can I just simply truncate the part out of the
 > primary box and put it back into the image position in the primary
 > box? Based on my experience for small molecule simulations, this needs
 > carefulness to deal with the inter and intra interactions. I am not
 > sure how CHARMm deal with it.
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 Rick Venable           29/500
 FDA/CBER/OVRR Biophysics Lab
 1401 Rockville Pike    HFM-419
 Rockville, MD  20852-1448  U.S.A.
 (301) 496-1905   Rick_Venable^at^nih.gov
 ALT email:  rvenable^at^speakeasy.org
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 "Don't blame me, I voted for Kang."
                          Homer
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