Hello all,

I'm trying to figure out= the best/easiest/least computationally expensive way of finding the absolu= te energy minimum of an organic molecule in gaussian09.

The way I've come to understand things is that there are 3 or 4 o= ptions:

1- Scan coordinates without optimization (= using Z matrix)=C2=A0

**I haven't personally tried this metho= d yet** but I'm wondering if such a scan is really representative of wh= at one wants to do.

2-Scan coordinates with optimi= zation (using redundant coordinates)

I have tried this method on = one coordinate but it is too computationally expensive if one wants to do 2= or 3 dihedral angles (the number of points is too large).

3-Produce a series of conformations using a conformational scan by= some software and then optimize them all.

I have personally trie= d this using "Maestro" but have found this to be extremely unsati= sfactory. In fact the geometries are rarely diverse enough and the geometry= isn't explored well enough no matter the options you pick.=C2=A0

4- Produce conormations manually and optimize them all.=

So far this has been my method of choice. It works well but it&#= 39;s annoying.

So in conclusion, my= questions are:

Do any of you know of a piece of s= oftware or a script that can produce/explore conformational space well enou= gh (I suppose it shouldn't be hard to write something like this but wha= t's the point if it already exists somewhere).=C2=A0

How do you procede in order to find global minima without wasting to= o much time and effort?

Thank you a= ll for reading this very long question.

=EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/=

--001a1133be5e401bca05135c4244-- From owner-chemistry@ccl.net Fri Apr 10 08:47:00 2015 From: "Rakesh Pant rakesh.pant**students.iiserpune.ac.in" To: CCL Subject: CCL: Error in Cluster Message-Id: <-51237-150410073907-16101-Gbv8AaAYXW+jrp71wHM5NQ|server.ccl.net> X-Original-From: Rakesh Pant Content-Type: multipart/alternative; boundary=001a1142751ed5982605135d355d Date: Fri, 10 Apr 2015 17:08:59 +0530 MIME-Version: 1.0 Sent to CCL by: Rakesh Pant [rakesh.pant{}students.iiserpune.ac.in] --001a1142751ed5982605135d355d Content-Type: text/plain; charset=UTF-8 Dear All, Can anyone suggest what could be the reason for below mentioned errors, which we observe in our cluster. Message from syslogd ~ gemini at Apr 10 17:07:23 ... kernel:[Hardware Error]: MC4_STATUS[Over|CE|MiscV|-|AddrV|-|-|CECC]: 0xdc084000ed080813 Message from syslogd ~ gemini at Apr 10 17:07:23 ... kernel:[Hardware Error]: Northbridge Error (node 2): DRAM ECC error detected on the NB. Message from syslogd ~ gemini at Apr 10 17:07:23 ... kernel:[Hardware Error]: cache level: L3/GEN, mem/io: MEM, mem-tx: RD, part-proc: SRC (no timeout) Thanks, Rakesh -- --001a1142751ed5982605135d355d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear All,

Can anyone suggest = what could be the reason for below mentioned errors, which we observe in ou= r cluster.

Message from syslogd ~ gemini at Apr 10 17:07:23 ...
=C2= =A0kernel:[Hardware Error]: MC4_STATUS[Over|CE|MiscV|-|AddrV|-|-|CECC]: 0xd= c084000ed080813

Message from syslogd ~ gemini at Apr 10 17:07:23 ...=C2=A0kernel:[Hardware Error]: Northbridge Error (node 2): DRAM ECC error= detected on the NB.

Message from syslogd ~ gemini at Apr 10 17:07:23 = ...
=C2=A0kernel:[Hardware Error]: cache level: L3/GEN, mem/io: MEM, mem= -tx: RD, part-proc: SRC (no timeout)

Thanks,

Rakesh

--001a1142751ed5982605135d355d-- From owner-chemistry@ccl.net Fri Apr 10 09:22:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor ~ fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Can/should you use the same checkpoint file for different geometries of a same molecule? Message-Id: <-51238-150410091024-16722-sGpDLK6s7hQEu9gfCShCAg**server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 10 Apr 2015 15:03:55 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]=[fluor.quimica.uniovi.es] On Fri, Apr 10, 2015 at 12:12:46PM +0200, ashika torikora ashika.torikora#gmail.com wrote: > Suppose one was optimizing different geometries of the same molecule. > Should one use the same checkpoint file (guess=read) for all these > geometries or should a completely new optimization be done? Ashika, 1) I've not used gaussian for many months, so take my advise with care 2) You can use the geometry of a checkpoint to start the calculation of another geometry. This can be a bad decission if you want to optimize different conformers of the same compountd, but if you control how to deform the initial geometry to start the optimization of the new conformer your computational chain can be efficient. I don't have gaussian examples at hand to show you but I've used this technique succesfully. 3) Another method would be using a structure editor (avogadro, jmol,...) to deform appropriately your initial geometry and using the same tool to write for you the input of the statical/dynamical code (quantum/classical) code of your election. Good luck, Dr. V�ctor Lua�a -- . . DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: / `' \ "I think the problem, to be quite honest with you, /(o)(o)\ is that you have never actually known what the question is." /`. \/ .'\ / '`'` \ "Lo mediocre es peor que lo bueno, pero tambi�n es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.V�ctor Lua�a ! Mediocre is worse than ! Departamento de Qu�mica F�sica y Anal�tica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor]![fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Fri Apr 10 11:03:01 2015 From: "Herbert Fruchtl herbert.fruchtl . st-andrews.ac.uk" To: CCL Subject: CCL: Error in Cluster Message-Id: <-51239-150410110203-7308-DBsI8WNQQN3+DfoQ711M8A]|[server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Fri, 10 Apr 2015 16:00:53 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl : st-andrews.ac.uk] This s not a computational chemistry question. You have faulty memory in your computer. Herbert On 10/04/15 12:38, Rakesh Pant rakesh.pant**students.iiserpune.ac.in wrote: > Dear All, > > Can anyone suggest what could be the reason for below mentioned errors, which we > observe in our cluster. > > Message from syslogd*o*gemini at Apr 10 17:07:23 ... > kernel:[Hardware Error]: MC4_STATUS[Over|CE|MiscV|-|AddrV|-|-|CECC]: > 0xdc084000ed080813 > > Message from syslogd*o*gemini at Apr 10 17:07:23 ... > kernel:[Hardware Error]: Northbridge Error (node 2): DRAM ECC error detected > on the NB. > > Message from syslogd*o*gemini at Apr 10 17:07:23 ... > kernel:[Hardware Error]: cache level: L3/GEN, mem/io: MEM, mem-tx: RD, > part-proc: SRC (no timeout) > > Thanks, > Rakesh > > > > -- > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Apr 10 11:54:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor||fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: What are the most efficient ways of finding an absolute energy minimum implemented in gaussian09? Message-Id: <-51240-150410113101-2329-ff+hO6x7t1ci9eNNFkVyZw!=!server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 10 Apr 2015 17:24:33 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor-$-fluor.quimica.uniovi.es] On Fri, Apr 10, 2015 at 12:30:52PM +0200, ashika torikora ashika.torikora_-_gmail.com wrote: > I'm trying to figure out the best/easiest/least computationally expensive > way of finding the absolute energy minimum of an organic molecule in > gaussian09. Ashika, 1) Your problem is 'global optimization' 2) There are several well studied algorithms: swarm methods, basin hoping, annealing, genetic algs, ... 3) Lok for literature on optimization algorithms, particularly global optimization methods. 4) Start gaining experience with non-quantum calculations: something much less expensive in computer time. Good luck, Dr. V�ctor Lua�a -- . . DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: / `' \ "I think the problem, to be quite honest with you, /(o)(o)\ is that you have never actually known what the question is." /`. \/ .'\ / '`'` \ "Lo mediocre es peor que lo bueno, pero tambi�n es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.V�ctor Lua�a ! Mediocre is worse than ! Departamento de Qu�mica F�sica y Anal�tica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor]-[fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Fri Apr 10 12:31:01 2015 From: "Adam Tenderholt atenderholt_-_gmail.com" To: CCL Subject: CCL: Density of States with ORCA Message-Id: <-51241-150410122722-31573-kL9rNYBxAPqsiWoHq2Pxww(~)server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=001a1134f2c0c466660513613c1b Date: Fri, 10 Apr 2015 09:26:55 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt-.-gmail.com] --001a1134f2c0c466660513613c1b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Subbu, I believe AOMix does what you describe. I also wrote QMForge for this very analysis, and have extended it over the years to include analysis of geometry optimizations, frequency calculations, and excited state calculations such as TD-DFT. You can find more information at http://qmforge.sourceforge.net. Best regards, Adam On Thu, Apr 9, 2015 at 9:55 PM, Subrahmanyam Sappati subrahmanyamsappati:-: gmail.com wrote: > Hi Jim & Deal All, > > Is it possible to get information/contribution of d-states (dxy, dyz, > dzx, dx2-y-2, dz2) for particular Eigen value (for e.g., HOMO, LUMO ) ? L= et > us suppose in Ru complex exaple, HOMO is contributing from Ru states. Now= , > whether one can get further information of d-states (such as contribution > of each d-states) to that HOMO level. > > Regards > Subbu > > On Fri, Apr 10, 2015 at 4:08 AM, Jim Kress jimkress35!^!gmail.com < > owner-chemistry|a|ccl.net> wrote: > >> >> Sent to CCL by: "Jim Kress" [jimkress35:+:gmail.com] >> Use AOMix >> >> http://www.sg-chem.net/aomix/ >> >> Jim >> >> >> -----Original Message----- >> > From: owner-chemistry+jimkress35=3D=3Dgmail.com _ ccl.net [mailto: >> owner-chemistry+jimkress35=3D=3Dgmail.com _ ccl.net] On Behalf Of Reinal= do >> Pis Diez pis_diez- -quimica.unlp.edu.ar >> Sent: Thursday, April 09, 2015 1:44 PM >> To: Kress, Jim >> Subject: CCL: Density of States with ORCA >> >> >> Sent to CCL by: Reinaldo Pis Diez [pis_diez\a/quimica.unlp.edu.ar] >> Gregorio, >> >> I don't know if you can get that information with a "single click". >> Instead, you could try the different options to the %output keyword to >> get Mulliken analysis of MOs in terms of atoms . Then, you should combin= e >> that information with the set of eigenvalues of your system and find the >> way to go from a discrete set of points to a continuous representation. >> >> Sorry for not being more specific. >> >> Regards, >> >> Reinaldo >> >> >> On 04/09/2015 07:06 AM, Gregorio Garc=C3=ADa Moreno gjgarcia-.-ujaen.es >> wrote: >> > >> > Sent to CCL by: =3D?UTF-8?B?R3JlZ29yaW8gR2FyY8OtYSBNb3Jlbm8=3D?=3D >> > [gjgarcia^_^ujaen.es] >> > Dear all >> > Does anyone know how to get density of states (of different molecular >> > fragments) from ORCA ouput files? >> > I know that MoCalc2012 software provides total density of States >> > (DOS), but i'm unable to obtain partial density of States thanks in >> > advance Gregorio >> > >> >> -- >> Reinaldo Pis Diez >> PhD in Chemistry >> Principal Researcher - CONICET (Argentina) Associated Professor - UNLP >> (Argentina) >> Email: pis_diez.at.quimica.unlp.edu.ar >> Tel: +54 221 424 0172http://www.ccl.net/chemis= try/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY|a|ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net or use>> >> >> > > > -- > > Subrahmanyam.Sappati > C/o Dr. Prasenjit Ghosh > IISER PUNE > Pin code : 411 008 > > Phone : +91 94 03 59 35 18 > > --001a1134f2c0c466660513613c1b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi Subbu,

I believe AOMix does what you= describe. I also wrote QMForge for this very analysis, and have extended i= t over the years to include analysis of geometry optimizations, frequency c= alculations, and excited state calculations such as TD-DFT. You can find mo= re information at http://qmforge= .sourceforge.net.

Best regards,

Adam

On Thu, Apr 9, 2015 at 9:55 PM, Subrahmanyam Sappa= ti subrahmanyamsappati:-:gmail.com <owner-chemistry^_^ccl.net> wrote:

Hi Jim & Deal All,

Is it possible to ge= t information/contribution of=C2=A0 d-states (dxy, dyz, dzx, dx2-y-2, dz2) = for particular Eigen value (for e.g., HOMO, LUMO ) ? Let us suppose in Ru c= omplex exaple, HOMO is contributing from Ru states. Now, whether one can ge= t further information of d-states (such as contribution of each d-states) t= o that HOMO level.

Regards
Subbu

On = Fri, Apr 10, 2015 at 4:08 AM, Jim Kress jimkress35!^!gmail.com <owner-chemistry|a|ccl.= net> wrote:

Sent to CCL by: "Jim Kress" [jimkress35:+:gmail.com]
Use AOMix

http://www.sg-c= hem.net/aomix/

Jim

-----Original Message-----
> From: owner-chemistry+jimkress35=3D=3Dgmail.com _ ccl.net [mailto:owner-chemistry+jimkress35=3D=3Dgmail.com _ ccl.net] On Behalf Of Reinaldo Pis Diez pis_diez- -quimica.unlp.edu.ar
Sent: Thursday, April 09, 2015 1:44 PM
To: Kress, Jim
Subject: CCL: Density of States with ORCA

Sent to CCL by: Reinaldo Pis Diez [pis_diez\a/quimica.unlp.edu.ar] Gregorio,

I don't know if you can get that information with a "single click&= quot;.
Instead, you could try the different options to the %output keyword to get = Mulliken analysis of MOs in terms of atoms . Then, you should combine that = information with the set of eigenvalues of your system and find the way to = go from a discrete set of points to a continuous representation.

Sorry for not being more specific.

Regards,

Reinaldo

On 04/09/2015 07:06 AM, Gregorio Garc=C3=ADa Moreno gjgarcia-.-ujaen.es
wrote:
>
> Sent to CCL by: =3D?UTF-8?B?R3JlZ29yaW8gR2FyY8OtYSBNb3Jlbm8=3D?=3D
> [gjgarcia^_^ujaen.es= ]
> Dear all
> Does anyone know how to get density of states (of different molecular<= br> > fragments) from ORCA ouput files?
> I know that MoCalc2012 software provides total density of States
> (DOS), but i'm unable to obtain partial density of States thanks i= n
> advance Gregorio
>

--
Reinaldo Pis Diez
PhD in Chemistry
Principal Researcher - CONICET (Argentina) Associated Professor - UNLP (Arg= entina)
Email: pis_diez.at.quimica.unlp.edu.ar

Tel: +54 221 424 0172 http://www.ccl.net/cgi-bin/= ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.= ccl.net/spammers.txt

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY|a|ccl.net or use:
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Subrahmanyam.Sappati
C/o= Dr. Prasenjit Ghosh
IISER P= UNE
Pin code : 411 008

= Phone : +91 94 03 59 35 18

--001a1134f2c0c466660513613c1b-- From owner-chemistry@ccl.net Fri Apr 10 13:06:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor!=!fluor.quimica.uniovi.es" To: CCL Subject: CCL: Torsional Representation Message-Id: <-51242-150410123916-7573-YwSyLB6OeBDL6x7zq6wVEg(a)server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 10 Apr 2015 18:32:49 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor++fluor.quimica.uniovi.es] On Tue, Apr 07, 2015 at 12:56:43AM -0400, Gulzar Singh gulzar.singh54 * gmail.com wrote: > > Sent to CCL by: "Gulzar Singh" [gulzar.singh54],[gmail.com] > Hi > I am writing a small tool to generate conformers of any given small molecule. > My idea was to get Z-matrix , change torsion, convert to Cartesian and get the conformer. > But Z-matrix does not always follow the bonds, it uses the 3D space but not the bonding pattern. > Is there any algorithm/tool (open source) which reports all torsions based on their respective four atoms? > OR > is there any other way to store these torsions? > OR > any other algorithm/logic (not any ready made tool) to generate conformers? Gulzar, 1) I'm not aware of any general tool already available. 2) There are two main methods to solve the orientation medhod in 3D: (a) quaternions, (b) rotation matrices. The classical description in terms of Euler angles produces known problems that must (and can) be avoided. Check literature on computer graphics and see the solutions already done. Good luck, Dr. V�ctor Lua�a -- . . DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: / `' \ "I think the problem, to be quite honest with you, /(o)(o)\ is that you have never actually known what the question is." /`. \/ .'\ / '`'` \ "Lo mediocre es peor que lo bueno, pero tambi�n es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.V�ctor Lua�a ! Mediocre is worse than ! Departamento de Qu�mica F�sica y Anal�tica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor|,|fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Fri Apr 10 13:41:00 2015 From: "Rakesh Pant rakesh.pant-.-students.iiserpune.ac.in" To: CCL Subject: CCL: Error in Cluster Message-Id: <-51243-150410131840-6515-w7Lxykb5uol4jCtYpVzWsQ]=[server.ccl.net> X-Original-From: Rakesh Pant Content-Type: multipart/alternative; boundary=047d7b414162458ac1051361f426 Date: Fri, 10 Apr 2015 22:48:34 +0530 MIME-Version: 1.0 Sent to CCL by: Rakesh Pant [rakesh.pant _ students.iiserpune.ac.in] --047d7b414162458ac1051361f426 Content-Type: text/plain; charset=UTF-8 Dear Sir, What are the possible solutions for it. Shall we replace memory modules. Thanks, On Fri, Apr 10, 2015 at 8:30 PM, Herbert Fruchtl herbert.fruchtl . st-andrews.ac.uk wrote: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl : st-andrews.ac.uk] > This s not a computational chemistry question. You have faulty memory in > your computer. > > Herbert > > > On 10/04/15 12:38, Rakesh Pant rakesh.pant**students.iiserpune.ac.in > wrote: > >> Dear All, >> >> Can anyone suggest what could be the reason for below mentioned errors, >> which we >> observe in our cluster. >> >> Message from syslogd*o*gemini at Apr 10 17:07:23 ... >> kernel:[Hardware Error]: MC4_STATUS[Over|CE|MiscV|-|AddrV|-|-|CECC]: >> 0xdc084000ed080813 >> >> Message from syslogd*o*gemini at Apr 10 17:07:23 ... >> kernel:[Hardware Error]: Northbridge Error (node 2): DRAM ECC error >> detected >> on the NB. >> >> Message from syslogd*o*gemini at Apr 10 17:07:23 ... >> kernel:[Hardware Error]: cache level: L3/GEN, mem/io: MEM, mem-tx: RD, >> part-proc: SRC (no timeout) >> >> Thanks, >> Rakesh >> >> >> >> -- >> >> > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > > -- Rakesh Pant Research Fellow IISER Pune, India --047d7b414162458ac1051361f426 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Dear Sir,

What are the possible sol= utions for it. Shall we replace memory modules.

Thanks,

On Fri, Ap= r 10, 2015 at 8:30 PM, Herbert Fruchtl herbert.fruchtl . st-andrews.ac.uk <owner-chemistry^^ccl.net&= gt; wrote:

Sent to CCL by: Herbert Fruchtl [herbert.fruchtl : st-andrews.ac.uk]
This s not a computational chemistry question. You have faulty memory in yo= ur computer.

=C2=A0 Herbert

On 10/04/15 12:38, Rakesh Pant rakesh.pant**students.iiserpune.ac.in wrote:
Dear All,

Can anyone suggest what could be the reason for below mentioned errors, whi= ch we
observe in our cluster.

Message from syslogd*o*gemini at Apr 10 17:07:23 ...
=C2=A0 kernel:[Hardware Error]: MC4_STATUS[Over|CE|MiscV|-|AddrV|-|-= |CECC]:
0xdc084000ed080813

Message from syslogd*o*gemini at Apr 10 17:07:23 ...
=C2=A0 kernel:[Hardware Error]: Northbridge Error (node 2): DRAM ECC error = detected
on the NB.

Message from syslogd*o*gemini at Apr 10 17:07:23 ...
=C2=A0 kernel:[Hardware Error]: cache level: L3/GEN, mem/io: MEM, mem-tx: R= D,
part-proc: SRC (no timeout)

Thanks,
Rakesh

--

--
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics
University of St Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532

-=3D This is automatically added to each message by the mailing script =3D-=
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Rakesh Pant

Research Fellow

IISER Pu= ne, India

--047d7b414162458ac1051361f426-- From owner-chemistry@ccl.net Fri Apr 10 14:16:00 2015 From: "Safiya Ess Amer amersaf85 .. yahoo.com" To: CCL Subject: CCL:G: Ghost_atoms_(symbol_Bq) Message-Id: <-51244-150410131906-6793-ltqFt6i13ZJPWLIF3GMtag=-=server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Fri, 10 Apr 2015 13:19:05 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85 _ yahoo.com] > "Safiya Amer amersaf85 ~~ yahoo.com" wrote: > > Sent to CCL by: Safiya Amer [amersaf85 ~~ yahoo.com] > ------=_Part_2658080_1212069801.1428507928881 > Content-Type: text/plain; charset=UTF-8 > Content-Transfer-Encoding: quoted-printable > > =C2=A0 =C2=A0 Thanks to reply=C2=A0Dr. Joshua Layfield. your Z-Matrix of H2= > -Fe(OH)3 was very useful for me. I used DFT (B3LYP and B3PW91) method and s= > ome basis set, also I used the same kayword that you used it in rout sectio= > n "POPT(z-matrix)", but there is problem in results, they were not as expec= > ted. I can not what is the reason. Can you advice me about any additional k= > aywords to get better results? > Thank you another=C2=A0Safiya AmerGraduate student > > =D9=85=D9=86: "Layfield, Joshua P. jlayfield**stthomas.edu" emistry]![ccl.net> > =D8=A5=D9=84=D9=89: "Amer, Safiya Ess " =20 > =D8=AA=D8=A7=D8=B1=D9=8A=D8=AE =D8=A7=D9=84=D8=A5=D8=B1=D8=B3=D8=A7=D9=84:= > =D8=A7=D9=84=D8=A3=D8=B1=D8=A8=D8=B9=D8=A7=D8=A1 25 =D9=85=D8=A7=D8=B1=D8= > =B3=D8=8C 2015=E2=80=8F 12:21 =D8=B5 > =D8=A7=D9=84=D9=85=D9=88=D8=B6=D9=88=D8=B9: CCL:G: Ghost atoms (symbol Bq) > =20 > > Sent to CCL by: "Layfield, Joshua P." [jlayfield _ stthomas.edu] > Safiya,=20 > > =C2=A0 If you want to do a partially optimized scan something like this sho= > uld > work.=C2=A0 (Please note that my method and geometry are not great).=C2=A0 = > By > defining the two hydrogen positions relative to the the dummy atom (xx) > you can scan the h2 molecule as a unit.=C2=A0 Also, if you want to do a fro= > zen > scan you also freeze the additional degrees of freedom at a good geometry > by adding the =C2=B3F=C2=B2 flag.=C2=A0 Hope this helps! > > > #HF/6-31G=C2=A0 =C2=A0 POPT(z-matrix) > > > Scanning the intermolecular distance between=C2=A0 Fe(OH)3 and H2 > > > 1 1 > fe > o=C2=A0 1 ofe2 > o=C2=A0 =C2=A0 1 ofe3=C2=A0 =C2=A0 =C2=A0 =C2=A0 2 ofeo3 > o=C2=A0 =C2=A0 1 ofe4=C2=A0 =C2=A0 =C2=A0 =C2=A0 2 ofeo4=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 3 dih4 > xx=C2=A0 =C2=A0 1 xxfe5=C2=A0 =C2=A0 =C2=A0 2 xxfeo5=C2=A0 =C2=A0 =C2=A0 = > =C2=A0 3 dih5 > h=C2=A0 =C2=A0 2 ho6=C2=A0 =C2=A0 =C2=A0 =C2=A0 1 hofe6=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 3 dih6 > h=C2=A0 =C2=A0 3 ho7=C2=A0 =C2=A0 =C2=A0 =C2=A0 1 hofe7=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 2 dih7 > h=C2=A0 =C2=A0 4 ho8=C2=A0 =C2=A0 =C2=A0 =C2=A0 1 hofe8=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 2 dih8 > h=C2=A0 =C2=A0 5 hxx9=C2=A0 =C2=A0 =C2=A0 =C2=A0 1 hxxfe9=C2=A0 =C2=A0 =C2= > =A0 =C2=A0 2 dih9 > h=C2=A0 =C2=A0 5 hxx10=C2=A0 =C2=A0 =C2=A0 1 hxxfe10 9 dih10 > > > ofe2=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.371600 > ofe3=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.371600 > ofeo3=C2=A0 =C2=A0 =C2=A0 109.471 > ofe4=C2=A0 =C2=A0 =C2=A0 =C2=A0 2.371600 > ofeo4=C2=A0 =C2=A0 =C2=A0 109.471 > dih4=C2=A0 =C2=A0 =C2=A0 =C2=A0 120.000 > xxfe5=C2=A0 =C2=A0 =C2=A0 2.000000 S 19 0.05 > xxfeo5=C2=A0 =C2=A0 =C2=A0 109.471 > dih5=C2=A0 =C2=A0 =C2=A0 -120.000 > ho6=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.947000 > hofe6=C2=A0 =C2=A0 =C2=A0 109.471 > dih6=C2=A0 =C2=A0 =C2=A0 =C2=A0 180.000 > ho7=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.947000 > hofe7=C2=A0 =C2=A0 =C2=A0 109.471 > dih7=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 0.000 > ho8=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.947000 > hofe8=C2=A0 =C2=A0 =C2=A0 109.471 > dih8=C2=A0 =C2=A0 =C2=A0 -180.000 > hxx9=C2=A0 =C2=A0 =C2=A0 =C2=A0 0.370000 f > hxxfe9=C2=A0 =C2=A0 =C2=A0 90.000=C2=A0 f > dih9=C2=A0 =C2=A0 =C2=A0 =C2=A0 180.000=C2=A0 f > hxx10=C2=A0 =C2=A0 =C2=A0 0.370000 f > hxxfe10=C2=A0 =C2=A0 =C2=A0 90.000=C2=A0 f > dih10 180.000=C2=A0 f > > > > Dr. Joshua Layfield > Assistant Professor, Department of Chemistry > University of St. Thomas > Maill # OSS 402 > 2115 Summit Ave.=20 > St. Paul, MN 55105-1079 > (651) 962-5577 > > > > > > > On 3/24/15, 12:00 PM, "Safiya Ess Amer amersaf85]~[yahoo.com" > wrote: > > > > >Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.com] > >Hello. > >Please, how can I use ghost atom with Cartesian coordinates? > >I have system of H2-Fe(OH)3 and use G03W for getting energy as function > >of=C2=A0=20 > >more distances (Z) from center of H2 to Fe atom. I am calculating now > >each=20 > >value of energy at some distance manually. I need to put ghost atom at > >center=20 > >of H2, how can I do that to get PES. > > > >Can anyone help me in input file? > >I have geometry of the system. > > > >Thanks in advance=20 > > > >Safiya Amer > >amersaf85]^[yahoo.com> > > > > > > -=3D This is automatically added to each message by the mailing script =3D- =C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 > =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0------ =_Part_2658080_1212069801.1428507928881 > Content-Type: text/html; charset=UTF-8 > Content-Transfer-Encoding: quoted-printable > >

mes new roman, new york, times, serif=E2=80=8F;font-size:24px">

ui_3_16_0_1_1428501633350_5610" style=3D"text-align: left;" dir=3D"ltr"> an>

lign: left;" dir=3D"ltr"> Helvetica Neue Light', 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande',= > sans-serif; font-size: 16px;" class=3D"" id=3D"yui_3_16_0_1_1428501633350_= > 6083"> Thanks to reply HelveticaNeue-Light, 'Helvetica Neue Light', 'Helvetica Neue', Helvetica, = > Arial, 'Lucida Grande', sans-serif; font-size: 16px;" class=3D"" id=3D"yui_= > 3_16_0_1_1428501633350_5865">Dr. Joshua Layfield. your Z-Matrix of H2-Fe(OH= > )3 was very useful for me. I used DFT (B3LYP and B3PW91) method and some ba= > sis set, also I used the same kayword that you used it in rout section " pan> , 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-siz= > e: 16px;" class=3D"" id=3D"yui_3_16_0_1_1428501633350_6231">POPT(z-matrix)"= > , but there is problem in results, they were not as expected. I can not wha= > t is the reason. Can you advice me about any additional kaywords to get bet= > ter results?

=3D"text-align: left;" dir=3D"ltr"> e-Light, 'Helvetica Neue Light', 'Helvetica Neue', Helvetica, Arial, 'Lucid= > a Grande', sans-serif; font-size: 16px;" class=3D"">

d=3D"yui_3_16_0_1_1428501633350_5610" style=3D"text-align: left;" dir=3D"lt= > r"> 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size= > : 16px;" class=3D"" id=3D"yui_3_16_0_1_1428501633350_6591">Thank you anothe= > r

= >

;" dir=3D"ltr">Safiya Amer

style=3D"text-align: left;" dir=3D"ltr">Graduate student

ui_3_16_0_1_1428501633350_5614">

div>

f=E2=80=8F; font-size: 24px;" id=3D"yui_3_16_0_1_1428501633350_5622">

style=3D"font-family: HelveticaNeue-Light, Helvetica Neue Light, Helvetica = > Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;" id=3D"= > yui_3_16_0_1_1428501633350_5621">

01633350_5620">

nt size=3D"2" face=3D"Arial" id=3D"yui_3_16_0_1_1428501633350_5619"> an style=3D"font-weight:bold;">=D9=85=D9=86: "Layfield, Joshua P= > . jlayfield**stthomas.edu" <owner-chemistry]![ccl.net>
le=3D"font-weight: bold;">=D8=A5=D9=84=D9=89: "Amer, Safiya Ess = > " <amersaf85]![yahoo.com>
350_6176"> 50_6175">=D8=AA=D8=A7=D8=B1=D9=8A=D8=AE =D8=A7=D9=84=D8=A5=D8=B1=D8=B3=D8= > =A7=D9=84: =D8=A7=D9=84=D8=A3=D8=B1=D8=A8=D8=B9=D8=A7=D8=A1 25 = > =D9=85=D8=A7=D8=B1=D8=B3=D8=8C 2015=E2=80=8F 12:21 =D8=B5
3_16_0_1_1428501633350_6292"> _16_0_1_1428501633350_6291">=D8=A7=D9=84=D9=85=D9=88=D8=B6=D9=88=D8=B9: an> CCL:G: Ghost atoms (symbol Bq)

sg_container" id=3D"yui_3_16_0_1_1428501633350_5623">

d=3D"yui_3_16_0_1_1428501633350_5624">

3_16_0_1_1428501633350_5625">Sent to CCL by: "Layfield, Joshua P." [jlayfie= > ld _ stthomas.edu]

50_5626">Safiya,

0_5627">

&= > nbsp; If you want to do a partially optimized scan something like this shou= > ld

work.&n= > bsp; (Please note that my method and geometry are not great). By
<= > /div>

defining the t= > wo hydrogen positions relative to the the dummy atom (xx)

=3D"ltr" id=3D"yui_3_16_0_1_1428501633350_5950">you can scan the h2 molecul= > e as a unit. Also, if you want to do a frozen

r" id=3D"yui_3_16_0_1_1428501633350_6054">scan you also freeze the addition= > al degrees of freedom at a good geometry

i_3_16_0_1_1428501633350_6009">by adding the =C2=B3F=C2=B2 flag. Hope= > this helps!

5">

div>

#HF/6-31G = > POPT(z-matrix)

633350_6057">

11">

Scanning the intermolecular distance between= > Fe(OH)3 and H2

33350_5743">

5">

1 1 >

= >

o 1 ofe2 >

o &nb= > sp; 1 ofe3 2 ofeo3

=3D"yui_3_16_0_1_1428501633350_6632"> o 1 ofe4 &n= > bsp; 2 ofeo4 3 dih4

"ltr" id=3D"yui_3_16_0_1_1428501633350_5661">xx 1 xxfe5 = > 2 xxfeo5 3 dih5

=3D"ltr" id=3D"yui_3_16_0_1_1428501633350_5662"> h 2 ho6 = > 1 hofe6 3 dih6

= >

h 3 h= > o7 1 hofe7 2 dih7 r>

h &n= > bsp; 4 ho8 1 hofe8 = > 2 dih8

h&= > nbsp; 5 hxx9 1 hxxfe9 = > 2 dih9

658"> h 5 hxx10 1 hxxfe10 9 dih10
v>

r=3D"ltr">

>ofe2 2.371600

ui_3_16_0_1_1428501633350_6611">ofe3 2.371600 >

ofeo3 = > 109.471

633350_5664">ofe4 2.371600

ltr">ofeo4 109.471

_3_16_0_1_1428501633350_5953">dih4 120.000
div>

xxfe5 &nb= > sp; 2.000000 S 19 0.05

_1428501633350_6614">xxfeo5 109.471

=3D"ltr" id=3D"yui_3_16_0_1_1428501633350_6630">dih5 -= > 120.000

ho= > 6 0.947000

3_16_0_1_1428501633350_6684">hofe6 109.471

iv dir=3D"ltr">dih6 180.000

"ltr">ho7 0.947000

ho= > fe7 109.471

_1_1428501633350_5802">dih7 0.000
v>

ho8 = > 0.947000

hofe8 = > 109.471

dih8 -180.000
<= > /div>

hxx9 &nb= > sp; 0.370000 f

428501633350_5643">hxxfe9 90.000 f

dir=3D"ltr" id=3D"yui_3_16_0_1_1428501633350_5644">dih9 = > ; 180.000 f

01633350_5645">hxx10 0.370000 f

tr" id=3D"yui_3_16_0_1_1428501633350_5646">hxxfe10 90.0= > 00 f

>dih10 180.000 f

633350_5631">

40">

<= > /div>

Dr. Joshua Lay= > field

Assi= > stant Professor, Department of Chemistry

i_3_16_0_1_1428501633350_5632">University of St. Thomas

=3D"ltr" id=3D"yui_3_16_0_1_1428501633350_5637">Maill # OSS 402

iv dir=3D"ltr" id=3D"yui_3_16_0_1_1428501633350_5636">2115 Summit Ave.
= >

St. Paul, MN = > 55105-1079

>(651) 962-5577

5633">

iv dir=3D"ltr">

5665">

On 3/24/15, 12:00 PM, "Safiya Ess Amer amersaf85]~[= > yahoo.com"

><owner-chemistry]*[ccl.net> wrote:

ui_3_16_0_1_1428501633350_5666">

_1_1428501633350_5959">>

28501633350_6687">>Sent to CCL by: "Safiya Ess Amer" [amersaf85||yahoo.c= > om]

>Hello.

>Plea= > se, how can I use ghost atom with Cartesian coordinates?

=3D"ltr">>I have system of H2-Fe(OH)3 and use G03W for getting energy as= > function

= > >of

>more distances (Z) from center = > of H2 to Fe atom. I am calculating now

3_16_0_1_1428501633350_6616">>each

>value = > of energy at some distance manually. I need to put ghost atom at

<= > div dir=3D"ltr" id=3D"yui_3_16_0_1_1428501633350_5667">>center
>

>of H2, how can= > I do that to get PES.

633350_5963">>

0_5964">>Can anyone help me in input file?

=3D"yui_3_16_0_1_1428501633350_5741">>I have geometry of the system.
= >

>
>

>Thanks in adva= > nce

><= > br>

>Safiya Amer

>ame= > rsaf85]^[yahoo.com>

633350_5669">>

= >

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i_3_16_0_1_1428501633350_6624">

v> > ------=_Part_2658080_1212069801.1428507928881-- > > I knew what is the problem. Regards Safiya Amer Graduate Student From owner-chemistry@ccl.net Fri Apr 10 14:51:01 2015 From: "John Keller jwkeller]-[alaska.edu" To: CCL Subject: CCL:G: What are the most efficient ways of finding an absolute energy minimum implemented in gaussian09? Message-Id: <-51245-150410125722-21741-1vdQ3j5UzuFP7IxXoX+Q5w\a/server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=047d7bdca1e40c31db051361a8ae Date: Fri, 10 Apr 2015 08:57:15 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller{:}alaska.edu] --047d7bdca1e40c31db051361a8ae Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable HyperChem has a very nice automated conformation search program that uses the Clark Still MCMM algorithm. See my YouTube video which illustrates how to do this with a dimethyl oxepane. https://www.youtube.com/watch?v=3DGBlojuz460Q The limitation is that one must use MM or PM3 theory. Then as you suggest re-optimize the various minima with Gaussian DFT or ab initio. John Keller On Fri, Apr 10, 2015 at 2:30 AM, ashika torikora ashika.torikora_-_gmail.co= m wrote: > Hello all, > > I'm trying to figure out the best/easiest/least computationally expensive > way of finding the absolute energy minimum of an organic molecule in > gaussian09. > > The way I've come to understand things is that there are 3 or 4 options: > > 1- Scan coordinates without optimization (using Z matrix) > **I haven't personally tried this method yet** but I'm wondering if such = a > scan is really representative of what one wants to do. > > 2-Scan coordinates with optimization (using redundant coordinates) > I have tried this method on one coordinate but it is too computationally > expensive if one wants to do 2 or 3 dihedral angles (the number of points > is too large). > > 3-Produce a series of conformations using a conformational scan by some > software and then optimize them all. > I have personally tried this using "Maestro" but have found this to be > extremely unsatisfactory. In fact the geometries are rarely diverse enoug= h > and the geometry isn't explored well enough no matter the options you pic= k. > > 4- Produce conormations manually and optimize them all. > So far this has been my method of choice. It works well but it's annoying= . > > > So in conclusion, my questions are: > > Do any of you know of a piece of software or a script that can > produce/explore conformational space well enough (I suppose it shouldn't = be > hard to write something like this but what's the point if it already exis= ts > somewhere). > > How do you procede in order to find global minima without wasting too muc= h > time and effort? > > > Thank you all for reading this very long question. > =EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/ > --047d7bdca1e40c31db051361a8ae Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

HyperChem has a very nice automated conformation sear= ch program that uses the Clark Still MCMM algorithm. See my YouTube video w= hich illustrates how to do this with a dimethyl oxepane.

https://www.youtube.com/= watch?v=3DGBlojuz460Q

The limitation is that one must use MM = or PM3 theory. Then as you suggest re-optimize the various minima with Gaus= sian DFT or ab initio.

John Keller

On Fri, Apr 10, 2015 = at 2:30 AM, ashika torikora = ashika.torikora_-_gmail.com <owner-chemistry(-)ccl.net> wrote:

Hello all,
I'm trying to figure out the best/easiest/least comput= ationally expensive way of finding the absolute energy minimum of an organi= c molecule in gaussian09.

The way I've come to= understand things is that there are 3 or 4 options:

1- Scan coordinates without optimization (using Z matrix)=C2=A0

**I haven't personally tried this method yet** but I'm wondering = if such a scan is really representative of what one wants to do.

2-Scan coordinates with optimization (using redundant coordi= nates)

I have tried this method on one coordinate but it is too c= omputationally expensive if one wants to do 2 or 3 dihedral angles (the num= ber of points is too large).

3-Produce a series of= conformations using a conformational scan by some software and then optimi= ze them all.

I have personally tried this using "Maestro&quo= t; but have found this to be extremely unsatisfactory. In fact the geometri= es are rarely diverse enough and the geometry isn't explored well enoug= h no matter the options you pick.=C2=A0

4- Produce= conormations manually and optimize them all.

So far this has bee= n my method of choice. It works well but it's annoying.

<= /div>

So in conclusion, my questions are:

Do any of you know of a piece of software or a script that can p= roduce/explore conformational space well enough (I suppose it shouldn't= be hard to write something like this but what's the point if it alread= y exists somewhere).=C2=A0

How do you procede in o= rder to find global minima without wasting too much time and effort?

<= div>

Thank you all for reading this very long = question.

=EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/

--047d7bdca1e40c31db051361a8ae-- From owner-chemistry@ccl.net Fri Apr 10 19:00:01 2015 From: "Ross Walker rcw(_)sdsc.edu" To: CCL Subject: CCL: Zing - Computational Chemical Biology Conference (Cairns Australia) Message-Id: <-51246-150410182729-17067-yt7IfumKgnEwkdgg6KdHbg]~[server.ccl.net> X-Original-From: "Ross Walker" Date: Fri, 10 Apr 2015 18:27:26 -0400 Sent to CCL by: "Ross Walker" [rcw.(~).sdsc.edu] Talk Consideration Deadline: 1st May 2015. Poster Submission Deadline: 1st June 2015 Dear Colleagues, We invite you to attend the Zing conference on Computational Chemical Biology Conference (http://www.zingconferences.com/conferences/computational-chemical-biology/) that myself and Prof. Ian Gould are chairing. The meeting will take place at the Pullman Cairns International Hotel from 6th 9th August 2015. Sponsored by Takeda, DE Gruyter, Royal Society of Chemistry and OpenEye. We have a number of exciting plenary and invited speakers lined up including a number of young and dynamic innovators from both academia and industry: Prof. Darrin York (Rutgers) Prof. Jonathan Essex (Southampton) Prof. Qiang Cui (Wisconsin) Dr. Felice Lightstone (LLNL) Dr. Zoe Cournia (BRFA Athens) Prof. Ron Dror (Stanford) Prof. Carlos Simmerling (Stony Brook) Dr. Andy Jennings (Takeda) Prof. Patricia Jennings (UCSD) Prof. Erik Lindahl (KTH Stockholm) Prof. Knut Teigen (Bergen) Prof. Steven Schwartz (Arizona) Prof. Jeremy Tame (Yokohama) Prof. Oscar Ces (Imperial College) Dr. Daniel Ormsby (Dotmatics) Prof. Laura Barter (Imperial College) Prof. Dave Winkler (CSIRO) Prof. Adrian Roitberg (UFL) Prof. David Minh (IIT) Prof. Thomas Cheatham (Utah) Prof. Alexey Onufriev (Virginia Tech) Prof. David Mobley (UCI) Dr. Tom Darden (OpenEye) Dr. Paul Hawkins (OpenEye) The conference will focus on multidisciplinary research that leverages computer simulation to address key questions crossing the physical sciences-life sciences/biomedical interface. In particular, the conference will feature sessions focusing on the development and application of novel and state-of-the-art computational tools and technology for solving major problems in the life and biomedical sciences. Topics will include advances in molecular dynamics simulation of enzymes; computational approaches to studying the interaction of drugs, drug transporters and signaling enzymes with lipid membranes; simulation of protein-protein interaction and multi-protein complex enzymatic systems; computational study of signaling pathways; new techniques in computational drug discovery as they apply to enzyme reactivity and dynamics; simulation of allosteric interactions; advances in multi-scale modeling; new techniques for direct simulation of reactivity in biological systems; and the impact of technological advances in computer hardware and software on the field of chemical biology. The conference will feature lectures by established leaders in the fields, as well as a specific focus on encouraging young and talented researchers to present both challenging questions and new ideas for solving them. The aim is to encourage a collegial atmosphere to promote stimulating and insightful discussion while enjoying the beauty of tropical Cairns, Australia. Deadlines for submissions is 1st May 2015 for Oral abstracts and 1st June 2015 for poster abstracts. For information on confirmed speakers, sponsors and how to register, please go to: http://www.zingconferences.com/conferences/computational-chemical-biology/ [http://tinyurl.com/nyblv7o] We hope you will be able to join us in Cairns. Kind Regards, Ross Walker & Ian Gould Chairs of the Computational Chemical Biology Conference 2015. /\ \/ |\oss Walker --------------------------------------------------------- | Associate Research Professor | | San Diego Supercomputer Center | | Adjunct Associate Professor | | Dept. of Chemistry and Biochemistry | | University of California San Diego | | NVIDIA Fellow | | http://www.rosswalker.co.uk | http://www.wmd-lab.org | | Tel: +1 858 822 0854 | EMail:- ross(~)rosswalker.co.uk | --------------------------------------------------------- Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.