From owner-chemistry@ccl.net Sun Jan 29 05:28:00 2006 From: "Alexander Martins Silva alex.msilva_._uol.com.br" To: CCL Subject: CCL: Calculations on a DRBL cluster Message-Id: <-30681-060128222552-13947-lky+hEg5/08k3IUVy/1BDw,,server.ccl.net> X-Original-From: Alexander Martins Silva Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 29 Jan 2006 00:30:55 +0000 MIME-Version: 1.0 Sent to CCL by: Alexander Martins Silva [alex.msilva#%#uol.com.br] Hi CCLers, I have installed a small linux cluster with the DRBL program (drbl.sourceforge.net). I can execute small parallel jobs with mpi and even short Gamess calculations. However, the parallel jobs stops without error message when these jobs require some hours of calculation. Even when I start serial jobs on each node the error is the same. The same job can stop at differents points. What's happening? How can I solve this? I'm using a Mandrake 10/Athlon XP 2600 server machine with Raid1, 10 P4 clients and a PLanet 24port/gigabit/switch. Any suggestion or advise is welcome. Thanks, Alexander. From owner-chemistry@ccl.net Sun Jan 29 08:55:01 2006 From: "t.frankcombe|chem.leidenuniv.nl" To: CCL Subject: CCL: OPT on large molecules Message-Id: <-30682-060129071056-15692-+ybpW+XdPKBbkNKIEMN4BA\a/server.ccl.net> X-Original-From: t.frankcombe%%chem.leidenuniv.nl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 29 Jan 2006 06:54:33 -0500 MIME-Version: 1.0 Sent to CCL by: t.frankcombe^chem.leidenuniv.nl If you look at the derivation of normal mode analysis, you can see that it assumes that the forces acting on the atoms are zero. So no, you cannot get reliable frequencies from geometries that have not been optimised at the level of theory (including basis set!) that you're using to calculate your second derivatives. Having said that, I've never played around with how frequencies and normal modes change as the geometry moves away from the optimised structure. They will be wrong, but I don't really know how much by. Quoting "David M. Close closed~!~etsu.edu" : > Sent to CCL by: "David M. Close" [closed(_)etsu.edu] > CCLers: > I have a question about the necessity of optimizations. I have uncovered > an effect experimentally that involves changes in large molecules. By large > I mean that even partial optimizations with modest basis sets take several > days. The effect involves charge migration from one region of the molecule > to another region. I would like to examine this effect with computations. > After a weeks work I still don't have an answer because of the times taken to > determine the optimized structures. > I realize that the correct approach is to do calculations on the optimized > structures. For example, it is necessary to do frequency calculations on the > optimized structures using the same basis sets in both calculations. But > what if one didn't use the optimized structures? Suppose one only used a > good guess at the optimized structure? Would this cause the later > calculations to be invalid? Or might they be good enough to at least decide > if the effect of interest is present and that actual > optimizations are worthwhile? > Regards, Dave Close.> > > > ------------------------------------------------- This mail sent using the Science Webmailer at Leiden University, The Netherlands From owner-chemistry@ccl.net Sun Jan 29 13:30:00 2006 From: "JAMES VIVIAN jamestvivian()msn.com" To: CCL Subject: CCL: MD software question. Message-Id: <-30683-060129123352-5277-QTFxv2D0Qumo+vtFwUoKQQ,server.ccl.net> X-Original-From: "JAMES VIVIAN" Content-Type: text/plain; format=flowed Date: Sun, 29 Jan 2006 12:33:45 -0500 Mime-Version: 1.0 Sent to CCL by: "JAMES VIVIAN" [jamestvivian++msn.com] Don: You're basically correct that at the conceptual & mathematical level, things are pretty straightforward; you need to create & store ~3*N coordinates for N particles, and F=ma tells the story. So you then need an integrator. And a force-field. And maybe a linked-list (Verlet), and some trickerly 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 in a car is a relatively small fraction of the whole beast. Once you factor in the GUI, the flexibility to elect different ensembles (NVT, NPT, uVT Grand Canonical...), different force field / energetic options, solvation, build in constraints, SHAKE, RATTLE, thermostats, 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 packages don't just stop at generating trajectories; they'll allow you to do 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 all the pieces in a shrink-wrapped package. >From: "Don Steiger sd00_2002::yahoo.com" >Reply-To: "CCL Subscribers" >To: "Vivian, James T " >Subject: CCL: MD software question. >Date: Sat, 28 Jan 2006 20:51:09 -0500 > >Sent to CCL by: "Don Steiger" [sd00_2002[-]yahoo.com] >I have an MD question. As far as I can tell, the equations/math that goes >into MD are fairly straight forward and short. Yet there are a lot of MD >packages, and all of them are very large. So what is in these packages >that makes them so large?> > > From owner-chemistry@ccl.net Sun Jan 29 14:04:00 2006 From: "Christopher Cramer cramer===chem.umn.edu" To: CCL Subject: CCL:G: AMSOL Question Message-Id: <-30684-060128224953-23132-xkixCz7+9YOc6dDPF7goJA-*-server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-2--865240507 Date: Sat, 28 Jan 2006 20:53:53 -0600 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Christopher Cramer [cramer[A]chem.umn.edu] --Apple-Mail-2--865240507 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Three issues. Two answered as an AMSOL developer, one as a sometime solvation meddler... 1) AMSOL's Z-matrix format is that used by AMPAC and MOPAC. It's described in lots of places, e.g., http://www.chem.cmu.edu/courses/ 09-560/docs/msi/modenv/D_Files.html#944883 (under subheading MOPAC). 2) One does not need to specify atomic partial charges in AMSOL unless one is using the EXTCM (external charge model) keyword to calculate generalized Born solvation free energies with user supplied charges. It is quite possible, however, that example input decks contain such charges. That is because a convenient way to generate a new input geometry is to cut and paste from the .log file of a previously completed calculation. In that case, the partial atomic charges from that prior calculation are indeed found at the end of each atom's line, but that information is not read in the absence of EXTCM. 3) Jim Kress suggested that Mark Gordon's effective fragment potential (EFP) as an option for a supermolecular solute, where the supermolecule is a cluster of solvent molecules about a central non- solvent-molecule solute. EFP is certainly designed specifically for the purpose of modeling such clusters, but it does NOT include charge transfer to the solute molecules when they are represented by the EFP. Only fully quantum solvent molecules can transfer charge to/from the solute. The EFP may be thought of as a tremendously sophisticated molecular mechanics description (including exchange repulsion, polarizability, etc.) of the explicit solvent molecules, but they do not carry partial charges (unless Mark and his co-workers have an extension that I haven't yet seen). It could certainly be added, in principle, but it introduces some trickiness associated with partial occupation numbers in the quantum MOs. Chris Cramer On Jan 28, 2006, at 6:59 PM, Jim Kress ccl_nospam[A]kressworks.com wrote: > Sent to CCL by: "Jim Kress" [ccl_nospam|*|kressworks.com] > Why don't you try the Fragment Method in GAMESS/ PCGAMESS? It was > specifically designed for system such as yours. > > Jim > >> -----Original Message----- >> From: Mark Zottola mzottola * gmail.com >> [mailto:owner-chemistry^ccl.net] >> Sent: Saturday, January 28, 2006 11:49 AM >> To: Kress, Jim >> Subject: CCL:G: AMSOL Question >> >> Sent to CCL by: Mark Zottola [mzottola||gmail.com] >> ------=_Part_11700_8950891.1138462191404 >> Content-Type: text/plain; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable >> Content-Disposition: inline >> >> I am exploring the behaviour of a modestly-sized molecule in >> water. As the PCM models for water are known to fail to >> account for charge transfer, the other ab initio method would >> be to include a solvation shell. As this molecule would >> require approximately 10 waters, I would like to get an >> initial answer much quicker than ab initio methods on such a >> system would allow. Since AMSOL is parameterized to account >> for charge transfer, etc., it seems the obvious choice to >> answer my questions. >> >> To that end, I have a few unresolved questions after reading the >> AMSOL >> manual: >> >> 1) How does one build the z-matrix format that is used in >> AMSOL? This is not the traditional z-matrix form used in >> Gaussian. I can build a z-matrix >> - the question is how does one build an AMSOL z-matrix? >> >> 2) There appears to be a vicious circle in the creation of >> an AMSOL input deck. The input deck requires charges from an >> AMSOL run in order to run th= e calculation. How does one >> get AMSOL charges before running an AMSOL job? = I am sure I >> am misunderstanding the situation, but not sure where my >> mis-understanding arises. >> >> Thanks for your help! >> >> >> Mark >> >> ------=_Part_11700_8950891.1138462191404 >> Content-Type: text/html; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable >> Content-Disposition: inline >> >>
I am exploring the behaviour of a modestly-sized >> molecule in water.&nb= sp; As the PCM models for water are >> known to fail to account for charge tra= nsfer, the other ab >> initio method would be to include a solvation shell.&nb= sp; >> As this molecule would require approximately 10 waters, I >> would like to= get an initial answer much quicker than ab >> initio methods on such a system= would allow.  Since >> AMSOL is parameterized to account for charge tran= sfer, >> etc., it seems the obvious choice to answer my questions. >>
>>
 
>>
To that end, I have a few unresolved questions after >> reading the AMSOL= manual:
 
>>
1)  How does one build the z-matrix format that is >> used in AMSOL?=   This is not the traditional z-matrix >> form used in Gaussian.  I = can build a z-matrix - the >> question is how does one build an AMSOL z-matrix= ?
>>
 
2)  There appears to be a vicious >> circle in the creation of an AM= SOL input deck.  The >> input deck requires charges from an AMSOL run in = order to >> run the calculation.  How does one get AMSOL charges >> before r= unning an AMSOL job?  I am sure I am >> misunderstanding the situation, b= ut not sure where my >> mis-understanding arises. =20
 
>>
Thanks for your help!
 
>>
 
Mark
>> >> ------=_Part_11700_8950891.1138462191404-- >> >> >> >> -= This is automatically added to each message by the mailing >> script =- To recover the email address of the author of the >> message, please change the strange characters on the top line >> to the ^ sign. You can also look up the X-Original-From: line >> in the mail header.> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> -+-+-+-+-+ >> >> >> >> >> >> > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer|-|pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-2--865240507 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Three issues. Two answered as an = AMSOL developer, one as a sometime solvation meddler...

1)=A0 AMSOL's Z-matrix = format is that used by AMPAC and MOPAC. It's described in lots of = places, e.g.,=A0http://www.chem.cmu.edu/courses/09-560/docs/msi/modenv/D_Files.h= tml#944883 (under subheading MOPAC).

2)=A0 One does not need to = specify atomic partial charges in AMSOL unless one is using the EXTCM = (external charge model) keyword to calculate generalized Born solvation = free energies with user supplied charges. It is quite possible, however, = that example input decks contain such charges. That is because a = convenient way to generate a new input geometry is to cut and paste from = the .log file of a previously completed calculation. In that case, the = partial atomic charges from that prior calculation are indeed found at = the end of each atom's line, but that information is not read in the = absence of EXTCM.

3)=A0 Jim Kress suggested = that Mark Gordon's effective fragment potential (EFP) as an option for a = supermolecular solute, where the supermolecule is a cluster of solvent = molecules about a central non-solvent-molecule solute. EFP is certainly = designed specifically for the purpose of modeling such clusters, but it = does NOT include charge transfer to the solute molecules when they are = represented by the EFP. Only fully quantum solvent molecules can = transfer charge to/from the solute. The EFP may be thought of as a = tremendously sophisticated molecular mechanics description (including = exchange repulsion, polarizability, etc.) of the explicit solvent = molecules, but they do not carry partial charges (unless Mark and his = co-workers have an extension that I haven't yet seen). It could = certainly be added, in principle, but it introduces some trickiness = associated with partial occupation numbers in the quantum = MOs.

Chris = Cramer


On Jan 28, = 2006, at 6:59 PM, Jim Kress ccl_nospam[A]kressworks.com wrote:

Sent to CCL by: "Jim Kress" = [ccl_nospam|*|kressworks.com]
Why don't you = try the Fragment Method in GAMESS/ PCGAMESS?=A0 It was
specifically designed for system such as yours.=A0

Jim

-----Original = Message-----
From: Mark Zottola mzottola * = gmail.com=A0
Sent: = Saturday, January 28, 2006 11:49 AM
To: Kress, = Jim=A0
Subject: CCL:G: AMSOL Question

Sent to = CCL by: Mark Zottola [mzottola||gmail.com]
Content-Type: text/plain; = charset=3DISO-8859-1
Content-Transfer-Encoding: = quoted-printable
Content-Disposition: = inline

I am exploring the behaviour of a modestly-sized = molecule in=A0
water.=A0 = As the PCM models for water are known to fail to=A0
account = for charge transfer, the other ab initio method would=A0
be to = include a solvation shell.=A0 = As this molecule would=A0
require = approximately 10 waters, I would like to get an=A0
initial = answer much quicker than ab initio methods on such a=A0
system = would allow.=A0 Since AMSOL = is parameterized to account=A0
for = charge transfer, etc., it seems the obvious choice to=A0
answer = my questions.

To that end, I have a few unresolved questions after = reading the AMSOL
manual:

1)=A0 How does one build the = z-matrix format that is used in=A0
=A0 This is not the = traditional z-matrix form used in=A0
=A0 I can build = a z-matrix
- the question is how does one = build an AMSOL z-matrix?

2)=A0 There appears to be a vicious = circle in the creation of=A0
an AMSOL = input deck.=A0 The input = deck requires charges from an=A0
AMSOL = run in order to run th=3D e calculation.=A0 How does one=A0
get = AMSOL charges before running an AMSOL job?=A0 =3D I am sure I=A0
am = misunderstanding the situation, but not sure where my=A0

Thanks for your help!



------=3D_Part_11700_8950891.1138462191404
Content-Type: text/html; = charset=3DISO-8859-1
Content-Transfer-Encoding: = quoted-printable
Content-Disposition: = inline

<div>I am exploring the behaviour of a = modestly-sized=A0
molecule in water.&nb=3D sp; As the PCM models = for water are=A0
known to fail to account for charge tra=3D nsfer, = the other ab=A0
initio method would be to include a solvation = shell.&nb=3D sp;=A0
As this = molecule would require approximately 10 waters, I=A0
would = like to=3D=A0 get an = initial answer much quicker than ab=A0
initio = methods on such a system=3D=A0 = would allow.&nbsp; Since=A0
AMSOL is = parameterized to account for charge tran=3D sfer,=A0
etc., it = seems the obvious choice&nbsp;to answer my questions.
</div>
<div>To = that end, I have a few unresolved questions after=A0
reading = the AMSOL=3D=A0 = manual:</div> <div>&nbsp;</div>=A0
=A0
used in AMSOL?=3D &nbsp; This is not the = traditional z-matrix=A0
form = used in Gaussian.&nbsp; I =3D can build a z-matrix - the=A0
question = is how does one build an AMSOL z-matrix=3D ?</div>=A0
=A0
circle = in the creation of an AM=3D SOL input deck.&nbsp; The=A0
input = deck requires charges from an AMSOL run in =3D order to=A0
run the = calculation.&nbsp; How does one get AMSOL charges=A0
before = r=3D unning an AMSOL job?&nbsp; I am sure I am=A0
=A0
=A0
=A0




-=3D This is automatically added = to each message by the mailing=A0
script = =3D- To recover the email address of the author of the=A0
message, = please change the strange characters on the top line=A0
to the ^ = sign. You can also look up the X-Original-From: line=A0
in the = mail header.> Conferences:=A0

Search = Messages: http://www.ccl.net/htdig=A0 (login: ccl,=A0
=A0
-+-+-+-+-+






=



-=3D This is = automatically added to each message by the mailing script =3D-
To recover the email address of the author of the = message, please change
the strange characters on = the top line to the |-| sign. You can also
look up = the X-Original-From: line in the mail header.

E-mail = to subscribers: CHEMISTRY|-|ccl.net= or use:

E-mail to administrators: CHEMISTRY-REQUEST|-|ccl.net = or use

Subscribe/Unsubscribe:=A0

Before posting, check wait time = at: http://www.ccl.net

http:/= /server.ccl.net/chemistry/announcements/conferences/

Search = Messages: http://www.ccl.net/htdig=A0 (login: ccl, Password: = search)

If your mail bounces from CCL with 5.7.1 error, = check:






--


Christopher J. Cramer

University of Minnesota

Department of Chemistry

207 Pleasant St. = SE

Minneapolis, MN 55455-0431

--------------------------

=

Phone:=A0 (612) 624-0859 || FAX:=A0 (612) 626-2006

Mobile: (952) = 297-2575

cramer|-|pollux.chem.umn.edu<= /FONT>

http://pollux.chem.umn.edu/~cr= amer

(website = includes information about the textbook "Essentials

=A0 =A0 of Computational = Chemistry:=A0 Theories and = Models, 2nd Edition")


=

= --Apple-Mail-2--865240507-- From owner-chemistry@ccl.net Sun Jan 29 15:17:04 2006 From: "Osman Guner osman:_:san.rr.com" To: CCL Subject: CCL: Search for nominations for the 2007 Herman Skolnik Award Message-Id: <-30685-060129142409-2476-hVpn5BHvFHq1Vx6yycB5DA^^^server.ccl.net> X-Original-From: "Osman Guner" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0003_01C624C0.241A9340" Date: Sun, 29 Jan 2006 10:38:27 -0800 MIME-Version: 1.0 Sent to CCL by: "Osman Guner" [osman#san.rr.com] This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C624C0.241A9340 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Herman Skolnik Award - Call for Nominations The ACS Division of Chemical Information established this Award to recognize outstanding contributions to and achievements in the theory and practice of chemical information science. The Award is named in honor of the first recipient, Herman Skolnik. By this Award, the Division of Chemical Information is committed to encouraging the continuing preparation, dissemination and advancement of chemical information science and related disciplines through individual and team efforts. Examples of such advancement include, but are not limited to, the following: * Design of new and unique computerized information systems; * Preparation and dissemination of chemical information; * Editorial innovations; * Design of new indexing, classification, and notation systems; * Chemical nomenclature; * Structure-activity relationships; and * Numerical data correlation and evaluation. * Advancement of knowledge in the field The Award consists of a $3000 honorarium and a plaque. The recipient is expected to give an address at the time of the Award presentation. In recent years, the Award Symposium has been organized by the recipient. Nominations for the Herman Skolnik Award should describe the nominee's contributions to the field of chemical information and should include supportive materials such as a biographical sketch and a list of publications and presentations. Three seconding letters are also required. Nominations and supporting material should be sent by email to me (ggrethe|comcast.net). Paper submissions are no longer acceptable. The deadline for nominations for the 2007 Herman Skolnik Award is June 1, 2006. Guenter Grethe, CINF Awards Chair ------=_NextPart_000_0003_01C624C0.241A9340 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

 

 

Herman = Skolnik Award – Call for Nominations

 <= /p>

The ACS Division of Chemical Information established this Award to recognize outstanding contributions to and achievements in the theory and practice of chemical information science. = The Award is named in honor of the first recipient, Herman Skolnik. =

By this Award, = the Division of Chemical Information is = committed to encouraging the continuing preparation, dissemination and advancement of chemical information science and related disciplines through individual = and team efforts. Examples of such advancement include, but are not limited = to, the following:

  • Design of new and unique computerized information systems; =
  • Preparation and dissemination of chemical information; =
  • Editorial innovations;
  • Design of new indexing, classification, and notation = systems;
  • Chemical nomenclature;
  • Structure-activity relationships; and
  • Numerical data correlation and evaluation. =
  • Advancement of knowledge in the field

The Award = consists of a $3000 honorarium and a plaque. The recipient is expected to give an address at = the time of the Award presentation. In recent years, the Award Symposium has = been organized by the recipient.

Nominations for = the Herman Skolnik Award should describe the nominee's contributions to the field = of chemical information and should include supportive materials such as a biographical sketch and a list of publications and presentations. Three seconding letters are also required. Nominations and supporting = material should be sent by email to me (ggrethe|comcast.net). Paper submissions are no longer acceptable. The deadline for nominations = for the 2007 Herman Skolnik Award is June 1, 2006.

Guenter = Grethe, CINF Awards Chair

 <= /p>

 

------=_NextPart_000_0003_01C624C0.241A9340-- From owner-chemistry@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-- From owner-chemistry@ccl.net Sun Jan 29 16:26:01 2006 From: "Bruce Palfey brupalf|*|umich.edu" To: CCL Subject: CCL: suggestions for manual docking and building Message-Id: <-30687-060129154147-5198-dZAAYqL1AYVv6agw14YamQ~~server.ccl.net> X-Original-From: Bruce Palfey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Sun, 29 Jan 2006 14:55:37 -0500 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu] Hi I was wondering if people could suggest a good program for manually and interactively building protein-ligand or nucleic acid-ligand complexes. Characteristics of the ideal program are: - Direct. I'd like to be able to grab one molecule and maneuver it into a position I think is interesting using simple, direct mouse and/ or keyboard controls. - Easily loaded. The molecules - either macro or micro - would most likely come from different pdb files, though support of other formats would also be helpful. A minimum of file preparation/conversion is desirable. - Intuitive. The students who pass through my lab should be able to just pick it up and go; we need a tool to support our research, rather than a system to dedicate our efforts to mastering. - Available for common cheap platforms. I'd like to use this on PC's in my lab or on my Mac laptop, or both. - Supports hardware stereo. It seems to me that that's the best way to build. - Free. Or cheap. Or at least a good value worthy of an investment. I welcome all suggestions, and will summarize what I learn. ciao, Bruce Palfey Department of Biological Chemistry University of Michigan Medical School Ann Arbor, MI 48109-0606 From owner-chemistry@ccl.net Sun Jan 29 17:01:00 2006 From: "Marcel Swart m.swart|few.vu.nl" To: CCL Subject: CCL: OPT on large molecules Message-Id: <-30688-060129154145-5171-IX+YKBGHv7Wf/+0/C13s6g]^[server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252; format=flowed Date: Sun, 29 Jan 2006 21:35:39 +0100 Mime-Version: 1.0 (Apple Message framework v553) Sent to CCL by: Marcel Swart [m.swart * few.vu.nl] On Saturday, January 28, 2006, at 09:55 PM, David M. Close closed~!~etsu.edu wrote: > I have a question about the necessity of optimizations. > I have uncovered an effect experimentally that involves changes in > large molecules. > By large I mean that even partial optimizations with modest basis sets > take several days. > The effect involves charge migration from one region of the molecule > to another region. > I would like to examine this effect with computations. After a weeks > work I still don't > have an answer because of the times taken to determine the optimized > structures. Of course it depends on the method you use (e.g. RHF, DFT or CCSD(T)) how long your optimization will take, and also on the program you use for it, but in the end, if you want to be able to understand the experimental effect, or be able to predict changes in it, you *will need* the optimized geometries, as well as the frequencies to show that you didn't end up in some sort of n-th order saddle point. Note that the convergence of the geometry depends largely on the type of coordinates you have chosen, where Cartesians are usually not such a good choice, and it is better to use natural internal coordinates, delocalized coordinates or our recently developed adapted delocalized coordinates. –––––––––––––––––––––––––––––––––––––––––––– 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 –––––––––––––––––––––––––––––––––––––––––––– Starting May 1, 2006: ICREA researcher at Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) –––––––––––––––––––––––––––––––––––––––––––– From owner-chemistry@ccl.net Sun Jan 29 18:42:00 2006 From: "Dr. Seth Olsen s.olsen1/a\uq.edu.au" To: CCL Subject: CCL:G: AMSOL Question Message-Id: <-30689-060129183057-20314-6EzMuIDat9IbTSE1t7eSYg,server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 30 Jan 2006 09:30:45 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1*o*uq.edu.au] Jim makes a good point here. Either the Effective Fragment Potential and the Fragment Molecular Orbital method are implemented in GAMESS. They will both likely do well, since the most important terms in the intermolecular perturbation tend to be the electrostatic ones. FMO also incorporates exchange effects, as well as polarization (EFP might do this too - I need to reread the reference). If your solute is larger than your solvent than you may be able to get quick results using FMO if you make good use of the GDDI parallelization. Cheers, Seth Jim Kress ccl_nospam[A]kressworks.com wrote: >Sent to CCL by: "Jim Kress" [ccl_nospam|*|kressworks.com] >Why don't you try the Fragment Method in GAMESS/ PCGAMESS? It was >specifically designed for system such as yours. > >Jim > > > >>-----Original Message----- >>From: Mark Zottola mzottola * gmail.com >>[mailto:owner-chemistry^ccl.net] >>Sent: Saturday, January 28, 2006 11:49 AM >>To: Kress, Jim >>Subject: CCL:G: AMSOL Question >> >>Sent to CCL by: Mark Zottola [mzottola||gmail.com] >>------=_Part_11700_8950891.1138462191404 >>Content-Type: text/plain; charset=ISO-8859-1 >>Content-Transfer-Encoding: quoted-printable >>Content-Disposition: inline >> >>I am exploring the behaviour of a modestly-sized molecule in >>water. As the PCM models for water are known to fail to >>account for charge transfer, the other ab initio method would >>be to include a solvation shell. As this molecule would >>require approximately 10 waters, I would like to get an >>initial answer much quicker than ab initio methods on such a >>system would allow. Since AMSOL is parameterized to account >>for charge transfer, etc., it seems the obvious choice to >>answer my questions. >> >>To that end, I have a few unresolved questions after reading the AMSOL >>manual: >> >>1) How does one build the z-matrix format that is used in >>AMSOL? This is not the traditional z-matrix form used in >>Gaussian. I can build a z-matrix >>- the question is how does one build an AMSOL z-matrix? >> >>2) There appears to be a vicious circle in the creation of >>an AMSOL input deck. The input deck requires charges from an >>AMSOL run in order to run th= e calculation. How does one >>get AMSOL charges before running an AMSOL job? = I am sure I >>am misunderstanding the situation, but not sure where my >>mis-understanding arises. >> >>Thanks for your help! >> >> >>Mark >> >>------=_Part_11700_8950891.1138462191404 >>Content-Type: text/html; charset=ISO-8859-1 >>Content-Transfer-Encoding: quoted-printable >>Content-Disposition: inline >> >>
I am exploring the behaviour of a modestly-sized >>molecule in water.&nb= sp; As the PCM models for water are >>known to fail to account for charge tra= nsfer, the other ab >>initio method would be to include a solvation shell.&nb= sp; >>As this molecule would require approximately 10 waters, I >>would like to= get an initial answer much quicker than ab >>initio methods on such a system= would allow.  Since >>AMSOL is parameterized to account for charge tran= sfer, >>etc., it seems the obvious choice to answer my questions. >>
>>
 
>>
To that end, I have a few unresolved questions after >>reading the AMSOL= manual:
 
>>
1)  How does one build the z-matrix format that is >>used in AMSOL?=   This is not the traditional z-matrix >>form used in Gaussian.  I = can build a z-matrix - the >>question is how does one build an AMSOL z-matrix= ?
>>
 
2)  There appears to be a vicious >>circle in the creation of an AM= SOL input deck.  The >>input deck requires charges from an AMSOL run in = order to >>run the calculation.  How does one get AMSOL charges >>before r= unning an AMSOL job?  I am sure I am >>misunderstanding the situation, b= ut not sure where my >>mis-understanding arises. =20
 
>>
Thanks for your help!
 
>>
 
Mark
>> >>------=_Part_11700_8950891.1138462191404-- >> >> >> >>-= This is automatically added to each message by the mailing >>script =- To recover the email address of the author of the >>message, please change the strange characters on the top line >>to the ^ sign. You can also look up the X-Original-From: line >>in the mail header.> Conferences: >>http://server.ccl.net/chemistry/announcements/conferences/ >> >>Search Messages: http://www.ccl.net/htdig (login: ccl, >>Password: search)> >>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >>-+-+-+-+-+> > > > > From owner-chemistry@ccl.net Sun Jan 29 19:16:01 2006 From: "Dr. Seth Olsen s.olsen1^uq.edu.au" To: CCL Subject: CCL: MD software question. Message-Id: <-30690-060129184000-20832-ZJlsyfeNbMsydqnUonUZig . server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 30 Jan 2006 09:39:53 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1,+,uq.edu.au] Even for MD packages that are not specifically designed for proteins, there are still complications that go beyond just solving Newton's equation. Since the number of pairs for interactions scales as N**2, it is usually best if more complicated algorithms are used for finding pairs between which to evaluate different terms. Electrostatics are long-range (i.e. you will want to evaluate these between many pairs), but vdW terms are much shorter (you don't need to many pairs - it would be foolish to evaluate Lennard-Jones terms between molecules 50 angstrom apart!). Of course bonded terms are 'short range', but you still need to build pair lists. For a good, clear & well written discussion I recommend Allen & Tildesley's 'Computer Simulation of Liquids'. It's older, but not outdated and the writing is quite clear and smooth (a huge bonus for a tekkie book). For biomolecular simulations, software packages usually have additional complication designed to tailor to these systems. I just bought 'Molecular Modeling and Simulation - an Interdisciplary Guide' and it's next on my reading list. The reviews on Amazon are good for this one. You should also be able to find good reviews in the literature. Many programs also have auxilliary programs to help in setting up your system prior to simulation (particularly if you are dealing with, for example, an unnatural amino acid or unparametrized ligand). A good example of these are the Antechamber or Xleap modules of Amber. For more detailed discussion, I must refer to someone more cognate than me. I'm just starting getting ready for MD. By training so far I do excited-state quantum chem. Cheers, Seth Don Steiger sd00_2002::yahoo.com wrote: >Sent to CCL by: "Don Steiger" [sd00_2002[-]yahoo.com] >I have an MD question. As far as I can tell, the equations/math that goes into MD are fairly straight forward and short. Yet there are a lot of MD packages, and all of them are very large. So what is in these packages that makes them so large?> > > > > From owner-chemistry@ccl.net Sun Jan 29 21:14:01 2006 From: "Joaquin Barroso Flores joaco_barroso|-|yahoo.com" To: CCL Subject: CCL:G: localisation of transition states with gaussian Message-Id: <-30691-060129210525-4314-uVCdIQxt2HWM8kRkE/FIQQ,server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-208253198-1138583119=:97693" Date: Sun, 29 Jan 2006 19:05:19 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso-,-yahoo.com] --0-208253198-1138583119=:97693 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, Have you consider using the ONIOM approach? you could set a different level of theory for the aromatic moiety, since based on my own experience DFT methods exhibit convergence problems when aromatic substituents are present from time to time. I hope this may help you good luck "b wafaa wafaab2(_)yahoo.fr" escribió: Sent to CCL by: b wafaa [wafaab2(_)yahoo.fr] --0-2071525535-1138445180=:27426 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, I am studing cycloaddition (Diels-alder, 1,3 dipolar) reactions using theoretical approaches and I find great difficulties to locate transition states when bulk substituents (phenyl groups) are present in the reagents. I use the options: B3LYP/6-31G(d) Opt(TS, Noeigentest, Maxcycle=500) freq . However, the convergence fails after 2 or 3 days of calculation ?. I need your help for overcoming this problem if you have ideas about other options or astutenesses available in gaussian 98W software. Thank you in advance. W. Benchouk Melle Wafaa BENCHOUK Laboratoire de Chimie Théorique et modélisation Moléculaire Département de Chimie, Faculté des Sciences, Université A. Belkaid de Tlemcen, B.P. 119,Tlemcen, 13000, ALGERIA Tél: + 213 43 28 63 49 poste 229 Fax: + 213 43 28 61 08 e-mail: benchouk_wafaa*o*yahoo.fr --------------------------------- Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta. --0-2071525535-1138445180=:27426 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit --------------------------------- Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez la version beta. --0-2071525535-1138445180=:27426--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt********************************************************** Q. Joaquín Barroso Flores Instituto de Química UNAM Correo Alterno: joaquin_barroso^correo.unam.mx ********************************************************** --------------------------------- Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-208253198-1138583119=:97693 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hello,
 
Have you consider using the ONIOM approach? you could set a different level of theory for the aromatic moiety, since based on my own experience DFT methods exhibit convergence problems when aromatic substituents are present from time to time. I hope this may help you
 
good luck


"b wafaa wafaab2(_)yahoo.fr" <owner-chemistry^ccl.net> escribió:
Sent to CCL by: b wafaa [wafaab2(_)yahoo.fr]
--0-2071525535-1138445180=:27426
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Dear CCLers,
I am studing cycloaddition (Diels-alder, 1,3 dipolar) reactions using theoretical approaches and I find great difficulties to locate transition states when bulk substituents (phenyl groups) are present in the reagents.
I use the options: B3LYP/6-31G(d) Opt(TS, Noeigentest, Maxcycle=500) freq . However, the convergence fails after 2 or 3 days of calculation ?.
I need your help for overcoming this problem if you have ideas about other options or astutenesses available in gaussian 98W software.
Thank you in advance.
W. Benchouk


Melle Wafaa BENCHOUK
Laboratoire de Chimie Théorique et modélisation Moléculaire
Département de Chimie, Faculté des Sciences,
Université A. Belkaid de Tlemcen, B.P. 119,Tlemcen, 13000, ALGERIA
Tél: + 213 43 28 63 49 poste 229
Fax: + 213 43 28 61 08
e-mail: benchouk_wafaa*o*yahoo.fr

---------------------------------
Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta.
--0-2071525535-1138445180=:27426
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

 
Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.
Téléchargez la version beta.
--0-2071525535-1138445180=:27426--


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**********************************************************
Q. Joaquín Barroso Flores

Instituto de Química UNAM
Correo Alterno: joaquin_barroso^correo.unam.mx
**********************************************************

Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx --0-208253198-1138583119=:97693-- From owner-chemistry@ccl.net Sun Jan 29 22:43:00 2006 From: "Andrew Fant fant(~)pobox.com" To: CCL Subject: CCL: MD software question. Message-Id: <-30692-060129203713-1920-vVnbMertR7Wom+XGkuQ5TA=-=server.ccl.net> X-Original-From: Andrew Fant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 29 Jan 2006 17:49:46 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Fant [fant]_[pobox.com] Mrcel and James both made good points that I won't bother duplicating here. One other thing to bear in mind is that while the math(s) involved in MD is relatively straightforward, doing it efficiently usually isn't. Even in single-threaded code, there are a whole constellation of tricks/shortcuts/advanced techniques that can make things go much faster (an order of magnitude or more) compared to what a naive undergrad might achieve left to their own devices. And when you get into parallel processing, it becomes even more hairy. Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant%%pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself