From owner-chemistry -x- at -x- ccl.net Sun Jan 29 15:51:01 2006 From: "Marcel Swart m.swart%x%few.vu.nl" To: CCL Subject: CCL: MD software question. Message-Id: <-30686-060129152311-26513-rtT1OHlLGJVqBW7/EztKpA^server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-2--802166317 Date: Sun, 29 Jan 2006 21:25:07 +0100 Mime-Version: 1.0 (Apple Message framework v553) Sent to CCL by: Marcel Swart [m.swart[*]few.vu.nl] --Apple-Mail-2--802166317 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed James already pointed out some indications for the very many number of MD programs around; but I think the major issue is the F in the F=3Dma equation, i.e. the force field. It is very difficult to construct a force field that is equally valid for all different kinds of systems that MD simulations are used on. For instance, there have been force fields suited for MD simulations of organic solutes (OPLS), or biosystems (AMBER, GROMOS, CHARMM), but also that are mainly for geometry optimizations of organic molecules (MM2, Dreiding, MMFF94), and many many more .. Please note that this is just my short-cut summary of the many force=20 fields around, so don't be offended if your favorite FF is not listed on it.. Of course, in the end, the best programs are those that allow to choose=20= between any of the most relevant ones without any problems.. On Sunday, January 29, 2006, at 08:10 PM, JAMES VIVIAN=20 jamestvivian()msn.com wrote: > Don: > You're basically correct that at the conceptual & mathematical level,=20= > things > are pretty straightforward; you need to create & store ~3*N=20 > coordinates for > N particles, and F=3Dma tells the story. So you then need an=20 > integrator. And > a force-field. And maybe a linked-list (Verlet), and some trickerly=20= > for > periodic-boundary conditions, etc.. But the core or heart of the MD > simulation remains a fairly brief chunk of code, much like the engine=20= > in a > car is a relatively small fraction of the whole beast. > > Once you factor in the GUI, the flexibility to elect different=20 > ensembles > (NVT, NPT, uVT Grand Canonical...), different force field / energetic > options, solvation, build in constraints, SHAKE, RATTLE, thermostats,=20= > etc., > then things tend to spawn. So to craft a generally multi-purpose MD > package, things tend to get unwieldly in a hurry. And a lot of=20 > packages > don't just stop at generating trajectories; they'll allow you to do=20= > some > degree of post-processing, maybe even allow you to evaluate a time > correlation function, etc.. > > So they end up being non-trivial and worth the $$$ when you assemble=20= > all the > pieces in a shrink-wrapped package. =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E m.swart ~~ few.vu.nl W http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 Starting May 1, 2006: ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2--802166317 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 James already pointed out some indications for the very many number of MD programs around; but I think the major issue is the F in the F=3Dma equation, i.e. the force field. It is very difficult to construct a force field that is equally valid for all different kinds of systems that MD simulations are used on. For instance, there have been force fields suited for MD simulations of organic solutes (OPLS), or biosystems (AMBER, GROMOS, CHARMM), but also that are mainly for geometry optimizations of organic molecules (MM2, Dreiding, MMFF94), and many many more .. Please note that this is just my short-cut summary of the many force fields around,=20 so don't be offended if your favorite FF is not listed on it.. Of course, in the end, the best programs are those that allow to choose between any of the most relevant ones without any problems.. On Sunday, January 29, 2006, at 08:10 PM, JAMES VIVIAN jamestvivian()msn.com wrote: Don: You're basically correct that at the conceptual & mathematical level, things=20 are pretty straightforward; you need to create & store ~3*N coordinates for=20 N particles, and F=3Dma tells the story. So you then need an integrator. And=20 a force-field. And maybe a linked-list (Verlet), and some trickerly for=20 periodic-boundary conditions, etc.. But the core or heart of the MD=20 simulation remains a fairly brief chunk of code, much like the engine in a=20 car is a relatively small fraction of the whole beast. Once you factor in the GUI, the flexibility to elect different ensembles=20 (NVT, NPT, uVT Grand Canonical...), different force field / energetic=20 options, solvation, build in constraints, SHAKE, RATTLE, thermostats, etc.,=20 then things tend to spawn. So to craft a generally multi-purpose MD=20 package, things tend to get unwieldly in a hurry. And a lot of packages=20 don't just stop at generating trajectories; they'll allow you to do some=20 degree of post-processing, maybe even allow you to evaluate a time=20 correlation function, etc.. So they end up being non-trivial and worth the $$$ when you assemble all the=20 pieces in a shrink-wrapped package. = Helvetica=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96 Courierdr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E = 1919,1919,FFFFm.swart ~~ few.vu.nl W=20 = 1919,1919,FFFFhttp://www.few.vu.nl/~swart= = Helvetica=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96 = Courier0000,= 4040,8080Starting May 1, 2006: = Courier0000,4040,8080 ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) = Helvetica000= 0,4040,8080=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= --Apple-Mail-2--802166317--