From chemistry-request@server.ccl.net Tue Feb 13 05:09:20 2001 Received: from info.cyf-kr.edu.pl (root@info.cyf-kr.edu.pl [149.156.4.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1DA9Fw18946 for ; Tue, 13 Feb 2001 05:09:19 -0500 Received: from kinga.cyf-kr.edu.pl (IDENT:8304@kinga.cyf-kr.edu.pl [149.156.2.32]) by info.cyf-kr.edu.pl (8.9.3/8.9.3) with ESMTP id LAA24989 for ; Tue, 13 Feb 2001 11:09:13 +0100 (MET) Received: (from mynowak@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id LAA07604; Tue, 13 Feb 2001 11:09:11 +0100 (MET) Date: Tue, 13 Feb 2001 11:09:10 +0100 (MET) From: Mateusz Nowak To: Subject: Pair list generation problem in GROMOS96 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL I'm trying to run a regular MD simulation in GROMOS96. My system is 107 aa protein in a box of SPC water with 4 NA+ ions added. PBC are applied, and the box sizes are ~ 4*5*6 nm. Bonds involving hydrogens are shaken. In an output i'm getting following warnings: NONBML: WARNING, NOT ALL EXCLUDED NEIGHBOUR WERE SCANNED IN THE PAIR-LIST NONBML: WARNING, NOT ALL THIRD NEIGHBOUR WERE SCANNED IN THE PAIR-LIST Kinetic and non-bonded potental energy terms are not being calculated ("nan" instead of a value) in an initial (t=0) step. In next steps pair list contains 0 elements instead of ~300000, as it is in initial step. According to manual this warning occures when cut-off for pair list construction (RCUTP) is not reasonably large. In my case it has 1.0 nm (acctually twin rang cut-off 1.0/1.6 is used). I tried to run the same simulation with pair list construction cut-off 1.2 and 1.6 nm, but the same warning occures. Has anybody experienced similar problem? Any help will be appreciated. Mateusz Nowak Jagiellonian Univ. Krakow POLAND