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--