AMBER Archive (2008)

Subject: AMBER: How to build a cubic box of a newly synthesized compound?

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Wed Dec 24 2008 - 00:34:13 CST

 Dear all,

      I'd like to perform a md simulation of a newly synthesized compound to calculate the dielectric constant. But before the md is carried out, a cubic box of the compound should be built with a reasonable density. But I don't know how to place the molecules in the box, such as orientation, relative position etc. Could someone please give me suggestions on how to do it conveniently?

Thanks very much for the time.
Happy Christmas day. 

----
Jeffrey

__________________________________________________
¸Ï¿ì×¢²áÑÅ»¢³¬´óÈÝÁ¿Ãâ·ÑÓÊÏä?
http://cn.mail.yahoo.com

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