From chemistry-request %-% at %-% ccl.net Mon Jan 19 12:23:53 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0JHNqc1000492 for ; Mon, 19 Jan 2004 12:23:52 -0500 Received: from cornell.edu (cs6711168-41.satx.rr.com [67.11.168.41]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i0JHOYgk020643; Mon, 19 Jan 2004 12:24:51 -0500 (EST) Message-ID: <400C12D1.70408*at*cornell.edu> Date: Mon, 19 Jan 2004 11:24:33 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry*at*ccl.net" Subject: Re: CCL:residue cross correlation References: <27031.1074268337*at*www53.gmx.net> <400B8020.4060108*at*chem.vu.nl> In-Reply-To: <400B8020.4060108*at*chem.vu.nl> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi all If one used CHARMm/CHARMM to calculate these trajectories, why can't one use CHARMm/CHARMM to analyse them? Richard Anton Feenstra wrote: > Bimo Ario Tejo wrote: > >> Dear all, >> >> I'm just wondering does anyone have a program to calculate residue >> cross-correlation (DCCM) of MD trajectories based on vectors (origin >> at mean atom >> position during simulation)? I need such a program that able to read any >> trajectories regardless what program used (CHARMM, Amber, Gromacs, >> etc.)... > > > AFAIK, there is no common trajectory format, not even one that is > recognized > by more than a few programs... ;-{ > What I do know, is that most programs can write pdb files, and also most > can read them again. Gromacs can recognize concatenated pdb files as a > trajectory, and can read and write it as a native format (although slower > than most other formats, and huge amounts of diskspace...) I'm not sure > which correlations you mean, but I'm pretty sure it is possible to > calculate > them with one of the many analysis tools of Gromacs. > >