From jkl@ccl.net Wed Jul 8 17:58:38 1992 Date: Wed, 8 Jul 1992 17:58:36 -0400 From: jkl@ccl.net To: chemistry@ccl.net Subject: Major backout of the list Status: R I have BAD news. You wonder why it is quiet on Comp.Chem.List? There is a major mess (in lieu of the better term) up. When I was at the Gordon Conference, something happened with the Computational Chemistry List (our network gurus were "improving" things). They improved the things so well that all messages to Comp. Chem. List sent AFTER June 28 (i.e., on 29th until this moment) were lost (I did not see them either). That's an improvement!!! Today they fixed it finaly (some of you got an empty message from the list). If you sent any message to the Computational Chemistry list (i.e., to chemistry@ccl.net) after or on the June 29th, please repost them. Only the chemistry@ccl.net was affected, chemistry-request, and jkl were OK. Sorry again. It was not my fault --- actually it was nobody's fault, though in the litigation driven America it is probably a crime to think that accidents still happen. Jan jkl@ccl.net Jan K. Labanowski, Ph.D., Senior Supercomputer Specialist Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From jkl@ccl.net Wed Jul 8 18:27:16 1992 Date: Wed, 8 Jul 1992 18:27:13 -0400 From: jkl@ccl.net To: chemistry@ccl.net Subject: Forcefields archives idea Status: R Dear Computational Chemists, At the Gordon Conference on Computational Chemistry (hash, I supposedly should not mention the name in public, excuse moi...) there was some informal discussion of making an electronically accessible depot of Force Field parameters. No, it is not my idea... The reasons given were that sometimes results of Molecular Mechanics/Dynamics calculations described in papers cannot be reproduced since the details of FF used are not given. At the same time, it is recognized that publishing zillions of FF parameters in each paper is not the solution, since it would inflate paper volume. What are the choices: the obvious one is to ask the author(s) for details of calculations. The other one is to make a repository FF parameters available through e-mail or ftp at some site. But how to do it? There are some standards for description of force fields specifically, as well as parameter data in general. But who knows standards? (No flames please...). And mostly, are there any standards flexible enough to accommodate the ever changing approaches to the FF mathematical form? In my humble opinion, we should make it simple yet rigorous and unambiguous enough so it is useful. I would like to initiate some discussion on this with a few comments and questions of mine to give it a spin. The description of force field consists of: 1. description of the mathematical form of the potential energy function, treatment of 1-3, 1-4, 1-5, etc. non-bonded interactions, special cases (e.g. H-bonds), combination rules for vdW, etc. 2. description of atom/bond types. This may be verbal, but has to be precise. The information on how these are assigned is not always trivial (e.g., precedence rules), but is always important. 3. list of parameters in some kind of a table which relates to 1. and 2. (with units !), 4. comments on derivation of the FF (experimental, ab initio, what data, what basis sets, CFF way or "manual" fitting. Now, do we need it? And, what about commercially derived FF --- are they proprietary, and if so, should the papers using them be published in reviewed journals or they fit the scope of the famous "Journal of Irreproducible Results"? Please, no flames, this is not a clear issue, since deriving force fields is costly but at the same time it is needed. Can you copyright or patent the number? Not now, and FF developers do not have much legal defence beside a contract(license). People in software companies, please speak up ! On the other hand, people in academia are frequently not eager [or absent-minded (:-)) ] to share their parameters either (should I mention the cases of well known papers were the parameters were not given --- sure not, I want to live few more years). So in short, we need to agree on some guidelines if we want to do it (the format of FF description and parameters), the way FF's are named and referred to (we all know how fluid the parameters of a given force field are sometimes. It would be nice to have some REFNO kind thing which refers to a given version of a force field located precisely in time and space...). References to papers where FF was applied? References to papers which list parameters for the first time? Your comments are greatly appreciated but please take a deep breath before you write something on this topic. Jan Labanowski Ohio Supercomputer Center jkl@ccl.net Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET