From chemistry-request ":at:" server.ccl.net Fri Jun 7 13:00:22 2002 Received: from denali.biochem.missouri.edu ([128.206.91.240]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g57H0ML03134 for ; Fri, 7 Jun 2002 13:00:22 -0400 Received: from localhost (berjanskii |-at-| localhost) by denali.biochem.missouri.edu (SGI-SGI-8.9.3/8.9.3) with SMTP id LAA52688 for ; Fri, 7 Jun 2002 11:40:03 -0500 (CDT) Date: Fri, 7 Jun 2002 11:40:02 -0500 (CDT) From: Mark Berjanskii To: chemistry $#at#$ ccl.net Subject: TEMP from CORREL in CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CHARMM users, Could you please help me to find answers for some of the following questions related to the TEMP routine in CORREL module of CHARMM? 1) Should I use coordinate trajectories (IUNCRD files from Dynamics routine) or velocity files (IUNVEL files from Dynamics routine) to determine temperature with CORREL? 2) If I should use velocity files, does the temperature determined by CORREL with coordinate trajectories have any meaning? 3) If I should use velocity files, is there a procedure in CHARMM to convert coordinate trajectories into velocity files? 4) Are there other ways to determine temperature / kinetic energy of a part of your system (not the whole system) from an already collected coordinate trajectory? Thank you, Mark Berjanskii Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall Columbia, MO 65211 email: mberjans(+ at +)coin.org