From owner-chemistry@ccl.net Mon Apr 13 07:51:01 2015 From: "ashika torikora ashika.torikora=gmail.com" To: CCL Subject: CCL:G: What are the most efficient ways of finding an absolute energy minimum implemented in gaussian09? Message-Id: <-51248-150413074640-18498-6GBhYxFA8M7B8DTAwtnzzQ*server.ccl.net> X-Original-From: ashika torikora Content-Type: multipart/alternative; boundary=001a11c235dc685736051399aaf8 Date: Mon, 13 Apr 2015 13:46:33 +0200 MIME-Version: 1.0 Sent to CCL by: ashika torikora [ashika.torikora a gmail.com] --001a11c235dc685736051399aaf8 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello again, Dear Victor, Just to clarify, I am aware of the existence of algorithms that allow global optimization. I've personally used simulated annealing before with a molecular mechanics force field. My question was more of a practical one: - I personally find that molecular mechanics aren't good enough to predict the global minimum. The global minimum found by a simulated annealing run using MM will most probably not correspond to a global minimum in ab initio type calculation. - I want practical and non-expensive ways of finding global minima in gaussian09. Dear John, Hyperchem's conformational search might be interesting. Is it fine enough to produce all significant conformers of a given molecule? The problem I had with Macromodel was that I wasn't able to produce all significat conformers. =EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/ 2015-04-10 18:57 GMT+02:00 John Keller jwkeller]-[alaska.edu < owner-chemistry%%ccl.net>: > HyperChem has a very nice automated conformation search program that uses > the Clark Still MCMM algorithm. See my YouTube video which illustrates ho= w > 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.com wrote: > >> Hello all, >> >> I'm trying to figure out the best/easiest/least computationally expensiv= e >> 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 point= s >> 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 enou= gh >> and the geometry isn't explored well enough no matter the options you pi= ck. >> >> 4- Produce conormations manually and optimize them all. >> So far this has been my method of choice. It works well but it's annoyin= g. >> >> >> 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 exi= sts >> somewhere). >> >> How do you procede in order to find global minima without wasting too >> much time and effort? >> >> >> Thank you all for reading this very long question. >> =EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/ >> > > --001a11c235dc685736051399aaf8 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello again,

Dear Victor,
Jus= t to clarify, I am aware of the existence of algorithms that allow global o= ptimization. I've personally used simulated annealing before with a mol= ecular mechanics force field. My question was more of a practical one:
- I personally find that molecular mechanics aren't good enough t= o predict the global minimum. The global minimum found by a simulated annea= ling run using MM will most probably not correspond to a global minimum in = ab initio type calculation.=C2=A0
- I want practical and non-expe= nsive ways of finding global minima in gaussian09.

Dear John,
Hyperchem's conformational search might be intere= sting. Is it fine enough to produce all significant conformers of a given m= olecule? The problem I had with Macromodel was that I wasn't able to pr= oduce all significat conformers.

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

2015-04-10 18:57 GMT+02:00 John Keller jwkelle= r]-[alaska.edu <owner-chemistry%%cc= l.net>:
HyperChem has a very nice automated conformation search program that use= s the Clark Still MCMM algorithm. See my YouTube video which illustrates ho= w to do this with a dimethyl oxepane.
The limitation is that one must use MM o= r PM3 theory. Then as you suggest re-optimize the various minima with Gauss= ian DFT or ab initio.
John Keller


On Fri, Apr 10, 2015 a= t 2:30 AM, ashika torikora ashika.torikora_-_gmail.com <owner-chemistry[= a]ccl.net> wrote:
Hello all,

I'm trying to f= igure out the best/easiest/least computationally expensive way of finding t= he 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 c= oordinates without optimization (using Z matrix)=C2=A0
**I haven&= #39;t personally tried this method yet** but I'm wondering if such a sc= an 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 computational= ly expensive if one wants to do 2 or 3 dihedral angles (the number of point= s is too large).

3-Produce a series of conformatio= ns 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 rarel= y diverse enough and the geometry isn't explored well enough no matter = the options you pick.=C2=A0

4- Produce conormation= s 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:

D= o any of you know of a piece of software or a script that can produce/explo= re conformational space well enough (I suppose it shouldn't be hard to = write something like this but what's the point if it already exists som= ewhere).=C2=A0

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


Thank you all for reading this very long question.
=EF= =BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/


--001a11c235dc685736051399aaf8-- From owner-chemistry@ccl.net Mon Apr 13 11:12:01 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor[a]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: <-51249-150413110851-30299-2t+iDqin8OgH0ZX0HMBKAQ##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: Mon, 13 Apr 2015 17:02:05 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor * fluor.quimica.uniovi.es] On Mon, Apr 13, 2015 at 01:46:33PM +0200, ashika torikora ashika.torikora=gmail.com wrote: > - I want practical and non-expensive ways of finding global minima in > gaussian09. Ashika, I would say that your wish is contradictoty or extremely difficult at least. Any global optimization method requires a significant amount of computational effort. The requirement of quantum techniques contradicts cheapness. There are many kinds of interaction potential techniques. ¿Are you sure you have explored all possible types for your actual problem? If you describe with some detail the final problem you are interested in maybe someone can provide a better advise. Best regards, Dr. Víctor Luaña -- . . 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 también es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. ! Mediocre is worse than ! Departamento de Química Física y Analítica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor[a]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 Mon Apr 13 11:46:00 2015 From: "Andy Prussia andy.prussia]=[gmail.com" To: CCL Subject: CCL:G: What are the most efficient ways of finding an absolute energy minimum implemented in gaussian09? Message-Id: <-51250-150413110045-29967-n8wt7cEuNgfDMtna2vqdeQ*server.ccl.net> X-Original-From: "Andy Prussia" Content-language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_029B_01D075D9.0AFF2230" Date: Mon, 13 Apr 2015 11:00:11 -0400 MIME-Version: 1.0 Sent to CCL by: "Andy Prussia" [andy.prussia#gmail.com] This is a multipart message in MIME format. ------=_NextPart_000_029B_01D075D9.0AFF2230 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Ashika, =20 Unless the conformational search is incomplete, which you can determine = (as a rule of thumb) if the global minimum was found >10, macromodel = likely is finding the significant conformers within its energy window = (of that particular force field). To quickly get the global minimum, = cluster the search results for a couple force fields and optimize a = representative from each cluster (for efficiency). That way you = don=E2=80=99t have to trust the relative energies from molecular = mechanics. I would be remiss, however, if I didn=E2=80=99t mention that = the optimized global minimum you find may not be the relevant conformer = for whatever process you are interested in. =20 Best of luck, =20 Andy Prussia =20 > From: owner-chemistry+andy.prussia=3D=3Dgmail.com:-:ccl.net = [mailto:owner-chemistry+andy.prussia=3D=3Dgmail.com:-:ccl.net] On Behalf = Of ashika torikora ashika.torikora=3Dgmail.com Sent: Monday, April 13, 2015 7:47 AM To: Prussia, Andrew Subject: CCL:G: What are the most efficient ways of finding an absolute = energy minimum implemented in gaussian09? =20 Hello again, =20 Dear Victor, Just to clarify, I am aware of the existence of algorithms that allow = global optimization. I've personally used simulated annealing before = with a molecular mechanics force field. My question was more of a = practical one: - I personally find that molecular mechanics aren't good enough to = predict the global minimum. The global minimum found by a simulated = annealing run using MM will most probably not correspond to a global = minimum in ab initio type calculation.=20 - I want practical and non-expensive ways of finding global minima in = gaussian09. =20 Dear John, Hyperchem's conformational search might be interesting. Is it fine = enough to produce all significant conformers of a given molecule? The = problem I had with Macromodel was that I wasn't able to produce all = significat conformers. =20 =EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/ =20 =20 2015-04-10 18:57 GMT+02:00 John Keller jwkeller]-[alaska.edu = >: 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.=20 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 =20 =20 On Fri, Apr 10, 2015 at 2:30 AM, ashika torikora = ashika.torikora_-_gmail.com = > wrote: Hello all, =20 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. =20 The way I've come to understand things is that there are 3 or 4 options: =20 1- Scan coordinates without optimization (using Z matrix)=20 **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. =20 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). =20 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 = enough and the geometry isn't explored well enough no matter the options = you pick.=20 =20 4- Produce conormations manually and optimize them all. So far this has been my method of choice. It works well but it's = annoying. =20 =20 So in conclusion, my questions are: =20 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 = exists somewhere).=20 =20 How do you procede in order to find global minima without wasting too = much time and effort? =20 =20 Thank you all for reading this very long question. =EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/ =20 =20 ------=_NextPart_000_029B_01D075D9.0AFF2230 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi Ashika,

 

Unless the conformational search is incomplete, which you can determine = (as a=C2=A0 rule of thumb) if the global minimum was found >10, = macromodel likely is finding the significant conformers within its = energy window (of that particular force field). To quickly get the = global minimum, cluster the search results for a couple force fields = =C2=A0and optimize a representative from each cluster (for efficiency). = That way you don=E2=80=99t have to trust the relative energies from = molecular mechanics. I would be remiss, however, if I didn=E2=80=99t = mention that the optimized global minimum you find may not be the = relevant conformer for whatever process you are interested = in.

 

Best of luck,

 

Andy Prussia

 

From:<= /b> = owner-chemistry+andy.prussia=3D=3Dgmail.com:-:ccl.net = [mailto:owner-chemistry+andy.prussia=3D=3Dgmail.com:-:ccl.net] On = Behalf Of ashika torikora = ashika.torikora=3Dgmail.com
Sent: Monday, April 13, 2015 7:47 = AM
To: Prussia, Andrew
Subject: CCL:G: What = are the most efficient ways of finding an absolute energy minimum = implemented in gaussian09?

 

Hello = again,

 

Dear Victor,

Just to clarify, I am aware of the existence of = algorithms that allow global optimization. I've personally used = simulated annealing before with a molecular mechanics force field. My = question was more of a practical one:

- I personally find that molecular mechanics aren't = good enough to predict the global minimum. The global minimum found by a = simulated annealing run using MM will most probably not correspond to a = global minimum in ab initio type = calculation. 

- I = want practical and non-expensive ways of finding global minima in = gaussian09.

 

Dear John,

Hyperchem's conformational search might be = interesting. Is it fine enough to produce all significant conformers of = a given molecule? The problem I had with Macromodel was that I wasn't = able to produce all significat conformers.

 

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

 

 

2015-04-10 18:57 GMT+02:00 John Keller jwkeller]-[alaska.edu <owner-chemistry(a)ccl.net>:

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. =

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.com <owner-chemistry[a]ccl.net> = 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 enough and the = geometry isn't explored well enough no matter the options you = pick. 

 

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 exists somewhere). 

 

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

 

 

Thank you all for reading this very long = question.

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

 

 

------=_NextPart_000_029B_01D075D9.0AFF2230-- From owner-chemistry@ccl.net Mon Apr 13 12:21:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor..fluor.quimica.uniovi.es" To: CCL Subject: CCL: What are the most efficient ways of finding an absolute energy minimum implemented in gaussian09? Message-Id: <-51251-150413113811-7200-7sPiFVvmRd63Dc49rb2IFw*_*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: Mon, 13 Apr 2015 17:31:25 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor(-)fluor.quimica.uniovi.es] On Mon, Apr 13, 2015 at 01:46:33PM +0200, ashika torikora ashika.torikora=gmail.com wrote: > Hello again, > > Dear Victor, > Just to clarify, I am aware of the existence of algorithms that allow > global optimization. I've personally used simulated annealing before with a > molecular mechanics force field. My question was more of a practical one: > - I personally find that molecular mechanics aren't good enough to predict > the global minimum. The global minimum found by a simulated annealing run > using MM will most probably not correspond to a global minimum in ab initio > type calculation. Ashika, Have you tried basin hoping? It is used for very complex problems in modelling clusters, proteins and problems with a huge ammount of local minima. The language of the method is beautiful and highly familiar for any person versed in chemical kinetics. You can look for Prof. DJ Wales, from Cambridge. Their group provides routines for implementing the basin hoping algorithm on top of any code. With some practice on any scripting language (matlab, python, ...) you can try it. For the Wales group web page: If you want to see the symmetry of a large group of LJ clusters: Best regards, Dr. Víctor Luaña From owner-chemistry@ccl.net Mon Apr 13 13:18:01 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: <-51252-150413131428-22064-Yjxfoes5uBH5mbqp05xMxg]-[server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=047d7bdca1e4b8ff2b05139e3ed9 Date: Mon, 13 Apr 2015 09:14:21 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller(!)alaska.edu] --047d7bdca1e4b8ff2b05139e3ed9 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Further comments: -The only way to approach this problem directly with G09 is with AIMD. The trajectories produced can be further analyzed statistically to determine residence times in different conformations, which are proportional to the free energy content of the conformations. -MD using MM or semi-empirical theory can also be used in a similar fashion= . -The problem of finding "the" global minimum is even worse than you indicate. That is because different model chemistries, or same method with different basis sets, may yield different answers as to which conformational minimum has the lowest energy! -The Hyperchem conformational search method can be run for hundreds or thousands of cycles until there is at least a 10-fold repetition of say the 20-most stable conformations. That is just "step one". "Step two" is using a higher level theory to analyze the geometry, energy and vibrations of each of these. "Step three" is to use the Second Law and the calculated energy differences to create a conformer distribution that would describe 99%, or 99.9%, of the molecules in a large sample. In the literature this is the way that the NMR properties of conformationally flexible molecules have been predicted, where the chemical shifts are weight-averaged based on the calculated distribution. -Was the YouTube video I provided helpful in showing how the Hyperchem method works? -There is no way to "prove" that you have identified all conformational minima. John Keller On Mon, Apr 13, 2015 at 3:46 AM, ashika torikora ashika.torikora=3Dgmail.co= m < owner-chemistry+/-ccl.net> wrote: > Hello again, > > Dear Victor, > Just to clarify, I am aware of the existence of algorithms that allow > global optimization. I've personally used simulated annealing before with= a > molecular mechanics force field. My question was more of a practical one: > - I personally find that molecular mechanics aren't good enough to predic= t > the global minimum. The global minimum found by a simulated annealing run > using MM will most probably not correspond to a global minimum in ab init= io > type calculation. > - I want practical and non-expensive ways of finding global minima in > gaussian09. > > Dear John, > Hyperchem's conformational search might be interesting. Is it fine enough > to produce all significant conformers of a given molecule? The problem I > had with Macromodel was that I wasn't able to produce all significat > conformers. > > =EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/ > > > 2015-04-10 18:57 GMT+02:00 John Keller jwkeller]-[alaska.edu < > owner-chemistry(a)ccl.net>: > >> HyperChem has a very nice automated conformation search program that use= s >> the Clark Still MCMM algorithm. See my YouTube video which illustrates h= ow >> 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 sugges= t >> 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.com 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 mole= cule >>> 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 suc= h >>> 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 computationall= y >>> expensive if one wants to do 2 or 3 dihedral angles (the number of poin= ts >>> 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 eno= ugh >>> and the geometry isn't explored well enough no matter the options you p= ick. >>> >>> 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 ex= ists >>> somewhere). >>> >>> How do you procede in order to find global minima without wasting too >>> much time and effort? >>> >>> >>> Thank you all for reading this very long question. >>> =EF=BC=BC(;=EF=BE=9F=E2=88=87=EF=BE=9F)/ >>> >> >> > --047d7bdca1e4b8ff2b05139e3ed9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Further comments:
-The only way to approach this probl= em directly with G09 is with AIMD. The trajectories produced can be further= analyzed statistically to determine residence times in different conformat= ions, which are proportional to the free energy content of the conformation= s.
-MD using MM or semi-empirical theory can also be used in a si= milar fashion.
-The problem of finding "the" global min= imum is even worse than you indicate. That is because different model chemi= stries, or same method with different basis sets, may yield different answe= rs as to which conformational minimum has the lowest energy!=C2=A0
-The Hyperchem conformational search method can be run for hundreds or th= ousands of cycles until there is at least a 10-fold repetition of say the 2= 0-most stable conformations. That is just "step one". "Step = two" is using a higher level theory to analyze the geometry, energy an= d vibrations of each of these. "Step three" is to use the Second = Law and the calculated energy differences to create a conformer distributio= n that would describe 99%, or 99.9%, of the molecules in a large sample. In= the literature this is the way that the NMR properties of conformationally= flexible molecules have been predicted, where the chemical shifts are weig= ht-averaged based on the calculated distribution.
-Was the YouTub= e video I provided helpful in showing how the Hyperchem method works?
=
-There is no way to "prove" that you have identified all con= formational minima.=C2=A0
John Keller

On Mon, Apr 13, 2015 at 3:46 AM, = ashika torikora ashika.torikora=3Dgmail.com <owner-chemistry+/-ccl.net> wrote:
Hello again,

Dear Vict= or,
Just to clarify, I am aware of the existence of algorithms th= at allow global optimization. I've personally used simulated annealing = before with a molecular mechanics force field. My question was more of a pr= actical one:
- I personally find that molecular mechanics aren= 9;t good enough to predict the global minimum. The global minimum found by = a simulated annealing run using MM will most probably not correspond to a g= lobal minimum in ab initio type calculation.=C2=A0
- I want pract= ical and non-expensive ways of finding global minima in gaussian09.

Dear John,
Hyperchem's conformational searc= h might be interesting. Is it fine enough to produce all significant confor= mers of a given molecule? The problem I had with Macromodel was that I wasn= 't able to produce all significat conformers.

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


2015-04-10 18:57 GMT+02:00 = John Keller jwkeller]-[alas= ka.edu <owner-chemistry(a)ccl.net>:
HyperChem has a very nice autom= ated conformation search program that uses the Clark Still MCMM algorithm. = See my YouTube video which illustrates how to do this with a dimethyl oxepa= ne.
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.
Jo= hn Keller


On Fri, Apr 10, 2015 at 2:30 AM, ashika torikora ashika.torikora_-= _gmail.com <owner-chemistry[a]ccl.net> wrote:
Hello all,

<= /div>
I'm trying to figure out the best/easiest/least computational= ly expensive way of finding the absolute energy minimum of an organic molec= ule in gaussian09.

The way I've c= ome 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 wond= ering 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 (t= he number of points is too large).

3-Produce a ser= ies of conformations using a conformational scan by some software and then = optimize them all.
I have personally tried this using "Maest= ro" but have found this to be extremely unsatisfactory. In fact the ge= ometries are rarely diverse enough and the geometry isn't explored well= enough no matter the options you pick.=C2=A0

4- P= roduce conormations manually and optimize them all.
So far this h= as 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 exists somewhere).=C2=A0

How do you proced= e in order 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)/



--047d7bdca1e4b8ff2b05139e3ed9-- From owner-chemistry@ccl.net Mon Apr 13 13:52:01 2015 From: "Ponnadurai Ramasami ramchemi(_)intnet.mu" To: CCL Subject: CCL: Virtual Conference on Computational Chemistry-2015 Message-Id: <-51253-150413131956-25806-fmzZuN+0ToVi1dYFAsVp/A * server.ccl.net> X-Original-From: "Ponnadurai Ramasami" Date: Mon, 13 Apr 2015 13:19:54 -0400 Sent to CCL by: "Ponnadurai Ramasami" [ramchemi*o*intnet.mu] Dear Sir/Madam, Greetings from Mauritius. A Virtual Conference (online conference) on Computational Chemistry will be organised by the Computational Chemistry Group of the University of Mauritius. This will be the third Virtual Conference. The Virtual Conference will be held from 1st to 31st August 2015. You are invited to submit an abstract to be considered for the Virtual Conference. Deadline: 15th May 2015. All topics related to Computational Chemistry may be considered. Please visit the website of the Conference and let me know if you need more details. http://sites.uom.ac.mu/vccc2015/ Looking forward for your participation. Prof Ponnadurai Ramasami Chairman of the Organising Committee How the virual conference will take place? There will be a call for abstracts. Scientific committee will evaluate suitability of each submitted abstract. For each accepted abstract, author/s will be invited to submit the presentation in MS Word, MS Powerpoint, PDF or any other relevant format. Some examples are: (1) PDF format (15-20 pages) (2) Powerpoint format (25-30 slides) (3) Video (10-15 minutes) Presentations will be displayed on the website (secured). Registered participants will be able to download all the presentations. Participants can ask questions by sending email/s (using the online platform) to the corresponding author for each e-presentation. When a participant sends an email, the same email is received by all the registered participants. However, it is the responsibility of the corresponding author to reply to the question/s being asked within 24 hours. When the corresponding author responds by replying the email, the same is received by all the participants. Full paper (optional) will be reviewed and accepted papers will be collected in the conference proceedings. From owner-chemistry@ccl.net Mon Apr 13 14:57:01 2015 From: "Partha Sengupta anapspsmo^^^gmail.com" To: CCL Subject: CCL: SLC6A4 Message-Id: <-51254-150413145508-31046-eqbexNY9/giggKLUfHlBDg.:.server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=089e013d119ac14be405139fa6f3 Date: Tue, 14 Apr 2015 00:25:01 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo|a|gmail.com] --089e013d119ac14be405139fa6f3 Content-Type: text/plain; charset=UTF-8 Friends, SLC6A4 solute carrier family 6 (neurotransmitter transporter), member 4 for molecular dynamics calculation? PSS -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --089e013d119ac14be405139fa6f3 Content-Type: text/html; charset=UTF-8
Friends,

SLC6A4 solute carrier family 6 (neurotransmitter transporter), member 4

for molecular dynamics calculation?

PSS

--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan
--089e013d119ac14be405139fa6f3--