From owner-chemistry@ccl.net Tue Dec 6 00:39:01 2011 From: "Dillen, Jan jlmd:-:sun.ac.za JLMD:-:sun.ac.za" To: CCL Subject: CCL:G: Getting ride of additional imaginary frecuencies Message-Id: <-45986-111206003028-29065-pIsjdgg6jmppsZvL45Adcw.:.server.ccl.net> X-Original-From: "Dillen, Jan " Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 6 Dec 2011 07:30:13 +0200 MIME-Version: 1.0 Sent to CCL by: "Dillen, Jan [jlmd]=[sun.ac.za]" IMHO, there are no artefacts when calculating the eigenvalues of the Hessian matrix with current software. If some frequencies are non-zero, then there is a problem. If the program is unable to recognise the modes as either translational or vibrational, your system is not at a stationary point, and the convergence criteria are not met. If the imaginary frequencies persist after taking corrective action, meaning that you make those criteria more stringent, animate the modes and have a look. If you freeze atoms, you will almost always end up with non-zero derivatives. Get yourself a program that can display them and make sure they only involve frozen atoms or get a program that handles the effect of constraints on the vibrational modes correctly. Jan -----Original Message----- > From: owner-chemistry+jlmd==sun.ac.za,,ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za,,ccl.net] On Behalf Of Arne Dieckmann adieckma+*+googlemail.com Sent: 05 December 2011 19:28 To: Dillen, Jan Subject: CCL:G: Getting ride of additional imaginary frecuencies Sent to CCL by: Arne Dieckmann [adieckma^googlemail.com] Those frquencies are just an artefact as long as they are < 50 cm^-1. Have a look at the Gaussian Reference, it's explained under the "freq" keyword if I remember correctly. Cheers, Arne On Dec 5, 2011, at 12:45 AM, "Carlos T Nieto eneas,+,usal.es" wrote: > > Sent to CCL by: "Carlos T Nieto" [eneas ~ usal.es] Hi, everybody > > One of the typical problems in a optimization is the appearrance of > additional imaginary frecuencies in optimization or transition state minimizations. > > Im an user of Jaguar. In many frequency calculations (DFT/B3LYP) i > obtain small negative frequencies, e.g. < -30 cm-1.It's very > frequently i obtained it in: > > - Solvent calculations > - Transition states when freezing atoms involved in it. It's to > optimize the different substituents. > > When this frequencies are associated with certain type of easy > identifiable displacement, i modify the geometry along the suspected > vibration and reoptimize. This works well. Nevertheless, the most > difficult cases is when the displacement is difficult (some type of > small apparent rotation where almost all atoms participate) i don't > know how to disturb it. It often appears when i freeze atoms, let's > say to block the atoms involved in a TS to add substituents and reoptimize or in solvent calculations. > > With this type of frequencies i've tried several ways, but inefficiently: > > - Disturbing bulky groups and reoptimizing. > - Some authors suggest it's a problem of the grid build up of the dft > process. I tried to change to fine or ultrafine type grids without success. > - Other opinion is that is a mathematical artefact and such > frequencies could be ignored. I've cheked a few publications and it's indicated. > - In Transition state searchs, the small negative frequency is the > eigenvector n 2. Trying to force to search along eigenvector 1 or > lowest eigenvector doesn't works again. > > So, What else can i do? I'm not sure if i'm doing something wrong... > Is there a way to getting rid of it? If not, May i accept the result > and ignore the small imaginary frequency? Other authors said that, > accepting this, it's not accurate taking the thermodinamic data from > the frequency calculations... > > Will be reportable my results ignoring this additional frecuencies? > Shall I indicate them? > > Ill appreciate all the ideas from you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Dec 6 01:14:00 2011 From: "Darpan Aulakh darpan.aulakh2011(_)gmail.com" To: CCL Subject: CCL: query on morokuma EDA Message-Id: <-45987-111205235836-22527-zd5Ei9k+Niz3MufhMLxLzg===server.ccl.net> X-Original-From: Darpan Aulakh Content-Type: multipart/alternative; boundary=bcaec520f72b5adefd04b3654911 Date: Mon, 5 Dec 2011 20:58:30 -0800 MIME-Version: 1.0 Sent to CCL by: Darpan Aulakh [darpan.aulakh2011/a\gmail.com] --bcaec520f72b5adefd04b3654911 Content-Type: text/plain; charset=ISO-8859-1 I want to carry out the Morokuma-Kitaura enery decomposition analysis on B3LYP/aug-cc-pvdz level. For that i have to use keyword GBASIS=ACCD and with that ISPHER=1 is must. But the morokuma calculation is not designed for ISPHER. please tell me what other keyword to be used. Is it possible to carry out the MEDA for DFT using Gamess? Looking forward to your response. --bcaec520f72b5adefd04b3654911 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

I want to carry out the Morokuma-Kitaura enery decompos= ition analysis=A0=A0on B3LYP/aug-cc-pvdz level. For that i have to use keyw= ord GBASIS=3DACCD and with that ISPHER=3D1 is must. But the morokuma calcul= ation is not designed for ISPHER. please tell me what other keyword to be u= sed. Is it possible to carry out the MEDA for =A0DFT using Gamess?=A0Lookin= g forward to your response.

 --bcaec520f72b5adefd04b3654911-- From owner-chemistry@ccl.net Tue Dec 6 01:49:00 2011 From: "Arne Dieckmann adieckma _ googlemail.com" To: CCL Subject: CCL:G: Getting ride of additional imaginary frecuencies Message-Id: <-45988-111206014346-6066-3hD+M80JwIAeAqR5tbLDBA/./server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Mon, 5 Dec 2011 22:43:37 -0800 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Arne Dieckmann [adieckma],[googlemail.com] The term "non-zero" always depends the accuracy and noise of the numerical methods you are employing (and second derivatives are calculated numerically). As far as I know, Jaguar is not doing some magic that would make it an exception. Although I have never used Jaguar myself, I am sure you can find some information about the threshold for "non-zero" frequencies in the manual or email the support. Arne On Dec 5, 2011, at 9:30 PM, Dillen, Jan jlmd:-:sun.ac.za JLMD:-:sun.ac.za wrote: > > Sent to CCL by: "Dillen, Jan [jlmd]=[sun.ac.za]" > IMHO, there are no artefacts when calculating the eigenvalues of the Hessian matrix with current software. If some frequencies are non-zero, then there is a problem. If the program is unable to recognise the modes as either translational or vibrational, your system is not at a stationary point, and the convergence criteria are not met. If the imaginary frequencies persist after taking corrective action, meaning that you make those criteria more stringent, animate the modes and have a look. > > If you freeze atoms, you will almost always end up with non-zero derivatives. Get yourself a program that can display them and make sure they only involve frozen atoms or get a program that handles the effect of constraints on the vibrational modes correctly. > > Jan > > -----Original Message----- >> From: owner-chemistry+jlmd==sun.ac.za::ccl.net [mailto:owner-chemistry+jlmd==sun.ac.za::ccl.net] On Behalf Of Arne Dieckmann adieckma+*+googlemail.com > Sent: 05 December 2011 19:28 > To: Dillen, Jan > Subject: CCL:G: Getting ride of additional imaginary frecuencies > > > Sent to CCL by: Arne Dieckmann [adieckma^googlemail.com] Those frquencies are just an artefact as long as they are < 50 cm^-1. Have a look at the Gaussian Reference, it's explained under the "freq" keyword if I remember correctly. > > Cheers, > Arne > > > On Dec 5, 2011, at 12:45 AM, "Carlos T Nieto eneas,+,usal.es" wrote: > >> >> Sent to CCL by: "Carlos T Nieto" [eneas ~ usal.es] Hi, everybody >> >> One of the typical problems in a optimization is the appearrance of >> additional imaginary frecuencies in optimization or transition state minimizations. >> >> Im an user of Jaguar. In many frequency calculations (DFT/B3LYP) i >> obtain small negative frequencies, e.g. < -30 cm-1.It's very >> frequently i obtained it in: >> >> - Solvent calculations >> - Transition states when freezing atoms involved in it. It's to >> optimize the different substituents. >> >> When this frequencies are associated with certain type of easy >> identifiable displacement, i modify the geometry along the suspected >> vibration and reoptimize. This works well. Nevertheless, the most >> difficult cases is when the displacement is difficult (some type of >> small apparent rotation where almost all atoms participate) i don't >> know how to disturb it. It often appears when i freeze atoms, let's >> say to block the atoms involved in a TS to add substituents and reoptimize or in solvent calculations. >> >> With this type of frequencies i've tried several ways, but inefficiently: >> >> - Disturbing bulky groups and reoptimizing. >> - Some authors suggest it's a problem of the grid build up of the dft >> process. I tried to change to fine or ultrafine type grids without success. >> - Other opinion is that is a mathematical artefact and such >> frequencies could be ignored. I've cheked a few publications and it's indicated. >> - In Transition state searchs, the small negative frequency is the >> eigenvector n 2. Trying to force to search along eigenvector 1 or >> lowest eigenvector doesn't works again. >> >> So, What else can i do? I'm not sure if i'm doing something wrong... >> Is there a way to getting rid of it? If not, May i accept the result >> and ignore the small imaginary frequency? Other authors said that, >> accepting this, it's not accurate taking the thermodinamic data from >> the frequency calculations... >> >> Will be reportable my results ignoring this additional frecuencies? >> Shall I indicate them? >> >> Ill appreciate all the ideas from you.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Tue Dec 6 04:05:00 2011 From: "Amina Ghomri ghomriamina++yahoo.fr" To: CCL Subject: CCL: non electrostatic terms calculation in PCM Model Message-Id: <-45989-111206034730-27857-Ei3E39QvJDuCFGkZrmOLdQ .. server.ccl.net> X-Original-From: "Amina Ghomri" Date: Tue, 6 Dec 2011 03:47:28 -0500 Sent to CCL by: "Amina Ghomri" [ghomriamina#%#yahoo.fr] How PCM model calculate the non electrostatic terms (dispertion, cavity and repultion) From owner-chemistry@ccl.net Tue Dec 6 08:02:00 2011 From: "quartarolo ~~ unical.it" To: CCL Subject: CCL:G: wb97XD in g09 Message-Id: <-45990-111206074740-25767-lph1d/9M5cpjiJA+e9QFsw++server.ccl.net> X-Original-From: quartarolo^_^unical.it Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 06 Dec 2011 13:47:30 +0100 MIME-Version: 1.0 Sent to CCL by: quartarolo*unical.it Dear Tobias, Thanks. I made what you suggested for wB97X but DFT-D3 tells "functional name unknown". In dftd3.f file wb97x is not parametrized. Is it possible to obtain the parameters in a "simple" way and how eventually? thanks in advance best regards domenico Quoting "Tobias Schwabe tobba]^[uni-muenster.de" : > > Sent to CCL by: Tobias Schwabe [tobba!^!uni-muenster.de] > Hi Quartarolo, > > On 12/01/2011 11:40 AM, quartarolo|a|unical.it wrote: >> Is there a way to define this parameter manually in the input file and >> eventually where to search for vdW radius of lutetium. > > I don't know if there is any way to specify a certain parameter for > DFT-D in G09. One idea would be to override the addition of the > dispersion correction to wB97XD at all (which, if I remember right, > is NOT just wB97X): you can do so by an IOps overlay (3/124), see > > http://www.gaussian.com/g_tech/g_iops/ov3.htm > > Then, you have the "pure" DFT energy. Afterwards you can use > Grimme's DFT-D3 program - available from > > http://toc.uni-muenster.de/DFTD3/getd3.html > > to add the missing dispersion term. I think, it has the parameters > you need. Be aware, that the different flavors of dispersion > correction might not be quite the same (I haven't checked), and by > this you kind of create your own new model chemistry. You might want > to test this on some reference data before applying it to an unknown > problem. Certainly, you cannot compare energies obtained like this > with "normal" wB97XD energies. > > Of course, this whole set up is only working for single point > energies and is rather inelegant. Maybe someone has another idea? > > Regards, > Tobiashttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. **** Riservatezza / Confidentiality **** In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio. From owner-chemistry@ccl.net Tue Dec 6 11:11:00 2011 From: "Sanjay Bharathwaj computationalchemist/./gmail.com" To: CCL Subject: CCL: MD Simulations Message-Id: <-45991-111206111000-24202-fmzZuN+0ToVi1dYFAsVp/A##server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=bcaec5215dfd579c2d04b36eaadb Date: Tue, 6 Dec 2011 17:09:52 +0100 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist**gmail.com] --bcaec5215dfd579c2d04b36eaadb Content-Type: text/plain; charset=ISO-8859-1 Dear Sir, I am new to molecular dynamics and i wish to understand it before i can start working on it. In this regard, does anyone can point me to the tutorials on various kinds of MD available and theoretical background. Best regards, Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --bcaec5215dfd579c2d04b36eaadb Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sir,=

I am new to molecular dynamics and=A0
i wish to unders= tand it before i can start working on it.

In this = regard, does anyone can point me to the
tutorials on various kind= s of MD available and=A0
theoretical background.=A0

Best regards,
Sanjay



=
--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharm= endra Institute of Technology,
India.
--bcaec5215dfd579c2d04b36eaadb-- From owner-chemistry@ccl.net Tue Dec 6 11:52:00 2011 From: "Marcel Swart marcel.swart]~[icrea.cat" To: CCL Subject: CCL: MD Simulations Message-Id: <-45992-111206114844-9589-8+TsXXAxM91YzPNeHCEPXQ()server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-7--861939637 Date: Tue, 6 Dec 2011 10:48:47 -0600 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Marcel Swart [marcel.swart|icrea.cat] --Apple-Mail-7--861939637 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Have a look at the following books: Computer simulation of molecular liquids Allen & Tildesley Clarendon Press, Oxford, 1987 Understanding molecular simulation Frenkel & Smit Academic Press, 1996 Marcel Swart On 06 Dec 2011, at 10:09, Sanjay Bharathwaj = computationalchemist/./gmail.com wrote: >=20 > Dear Sir, >=20 > I am new to molecular dynamics and=20 > i wish to understand it before i can start working on it. >=20 > In this regard, does anyone can point me to the > tutorials on various kinds of MD available and=20 > theoretical background.=20 >=20 > Best regards, > Sanjay >=20 >=20 >=20 > --=20 > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart---icrea.cat marcel.swart---udg.edu web http://www.marcelswart.eu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-7--861939637 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Have = a look at the following books:

Computer simulation of = molecular liquids
Allen & Tildesley
Clarendon = Press, Oxford, 1987

Understanding molecular = simulation
Frenkel & Smit
Academic Press, = 1996

Marcel Swart

On = 06 Dec 2011, at 10:09, Sanjay Bharathwaj = computationalchemist/./gmail.com wrote:


Dear Sir,

I am new to molecular dynamics and 
i wish to = understand it before i can start working on = it.

In this regard, does anyone can point me to = the
tutorials on various kinds of MD available and 
theoretical background. 

Best = regards,
Sanjay



--
Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra = Institute of Technology,
India.


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Institut de Qu=EDmica = Computacional
Universitat de Girona

Facultat de Ci=E8ncies
Campus = Montilivi
17071 Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart---udg.edu




= --Apple-Mail-7--861939637-- From owner-chemistry@ccl.net Tue Dec 6 12:27:01 2011 From: "Tobias Schwabe tobba\a/uni-muenster.de" To: CCL Subject: CCL: wb97XD in g09 Message-Id: <-45993-111206115023-17384-2X83GAVIEedvRl+Xn+blrQ^^server.ccl.net> X-Original-From: Tobias Schwabe Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 06 Dec 2011 17:49:46 +0100 MIME-Version: 1.0 Sent to CCL by: Tobias Schwabe [tobba*_*uni-muenster.de] Hi Domenico, On 12/06/2011 01:47 PM, quartarolo ~~ unical.it wrote: > Thanks. I made what you suggested for wB97X but DFT-D3 tells "functional > name unknown". In dftd3.f file wb97x is not parametrized. Is it possible > to obtain the parameters in a "simple" way and how eventually? Well, I am neither an expert for wB97XD nor the DFT-D3 program. But from inspecting the manual of DFT-D3 (section 1.4) you can find that one can specify customer parameters in a local parameter file "$HOME/.dft3dpar.". So, you should re-check the literature to find out how to set the parameters for wB97XD. My best guess is using s8 = 0 and version = 2. You want to use a model what is called "zero damping" in DFT-D3 language, because that's consistent with wB97DX, so a1 and a2 will be irrelevant. So, you are left with 3 parameters: s6 (should be 1), sr6 (this should also be 1 for wB97XD) and alpha (should be 12). The file then looks like: 1.0 1.0 0.000 1.0 12 2 But again, I don't know, whether it is that easy. You should cross-check with some data where you can evaluate wB97XD with G09. Good luck, Tobias From owner-chemistry@ccl.net Tue Dec 6 13:01:01 2011 From: "Daniel Fernando Coimbra danielfcoimbra()gmail.com" To: CCL Subject: CCL: query on morokuma EDA Message-Id: <-45994-111206120320-17384-oZK/3J9WR4n2ph98FALhQQ!^!server.ccl.net> X-Original-From: Daniel Fernando Coimbra Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 06 Dec 2011 15:02:11 -0200 MIME-Version: 1.0 Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra+/-gmail.com] As described in GAMESS-US Input Description document, page 192, Morokuma-Kitaura decomposition analisys is limited to closed shell RHF monomers.[1] We have successfully used LMOEDA for DFT using GAMESS-US. [1] http://www.msg.ameslab.gov/gamess/GAMESS_Manual/input.pdf On 06-12-2011 02:58, Darpan Aulakh darpan.aulakh2011(_)gmail.com wrote: > I want to carry out the Morokuma-Kitaura enery decomposition > analysis on B3LYP/aug-cc-pvdz level. For that i have to use keyword > GBASIS=ACCD and with that ISPHER=1 is must. But the morokuma calculation > is not designed for ISPHER. please tell me what other keyword to be > used. Is it possible to carry out the MEDA for DFT using > Gamess? Looking forward to your response. > -- Daniel Fernando Coimbra Grupo de Estrutura Eletrônica Molecular Departamento de Química Universidade Federal de Santa Catarina From owner-chemistry@ccl.net Tue Dec 6 13:37:00 2011 From: "Vincent Leroux vincent.leroux===loria.fr" To: CCL Subject: CCL: MD Simulations Message-Id: <-45995-111206121321-29055-1UidyRA/sBPQoQmJHSzGeA:-:server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 06 Dec 2011 18:13:04 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux _ loria.fr] Welcome to the MD field Sanjay! Old but still very good to understand the "logic": http://dx.doi.org/10.1002/anie.199009921 More up-to-date: http://dx.doi.org/10.1002/anie.200502655 Recommended reads: http://dx.doi.org/10.1007/s10822-011-9422-4 http://dx.doi.org/10.1126/science.1187409 http://dx.doi.org/10.1038/nsb0902-646 Tutorials, etc.: depends on which software you plan on using. If you are interested into NAMD, then go there: http://www.ks.uiuc.edu/Research/namd/ and check the Documentation section... Have fun :-) On 06/12/2011 17:09, Sanjay Bharathwaj computationalchemist/./gmail.com wrote: > > Dear Sir, > > I am new to molecular dynamics and > i wish to understand it before i can start working on it. > > In this regard, does anyone can point me to the > tutorials on various kinds of MD available and > theoretical background. > > Best regards, > Sanjay > > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. From owner-chemistry@ccl.net Tue Dec 6 14:11:00 2011 From: "=?iso-8859-1?B?THXtcyBQaW50byBkYSBTaWx2YQ==?= luist311_+_hotmail.com" To: CCL Subject: CCL: MD Simulations Message-Id: <-45996-111206114624-6900-TOHoiYrCKZlisJ8lkTVOSQ%x%server.ccl.net> X-Original-From: =?iso-8859-1?B?THXtcyBQaW50byBkYSBTaWx2YQ==?= Content-Type: multipart/alternative; boundary="_7ae486e1-db18-44db-a9a2-6528e437d248_" Date: Tue, 6 Dec 2011 16:46:14 +0000 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?B?THXtcyBQaW50byBkYSBTaWx2YQ==?= [luist311 .. hotmail.com] --_7ae486e1-db18-44db-a9a2-6528e437d248_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You have=2C for example=2C NAMD software and tutorials (http://www.ks.uiuc.= edu/Research/namd/). > From: owner-chemistry{}ccl.net To: luist311{}hotmail.com Subject: CCL: MD Simulations Date: Tue=2C 6 Dec 2011 17:09:52 +0100 Dear Sir=2C I am new to molecular dynamics and i wish to understand it before i can sta= rt working on it. In this regard=2C does anyone can point me to thetutorials on various kinds= of MD available and=20 theoretical background.=20 Best regards=2CSanjay --=20 Regards=2C Dr. Sanjay Bharathwaj Kumar=2C Dharmendra Institute of Technology=2C India. = --_7ae486e1-db18-44db-a9a2-6528e437d248_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
You have=2C for example=2C NAMD software and tutorials (http://www.ks.uiuc.= edu/Research/namd/).

From: owner-chemis= try{}ccl.net
To: luist311{}hotmail.com
Subject: CCL: MD Simulations
= Date: Tue=2C 6 Dec 2011 17:09:52 +0100


Dear Sir=2C

I am new to molecular dynamics and =3B
i wish to u= nderstand it before i can start working on it.

In = this regard=2C does anyone can point me to the
tutorials on vario= us kinds of MD available and =3B
theoretical background. =3B

Best regards= =2C
Sanjay


<= div>
--
Regards=2C
Dr. Sanjay Bharathwaj Kumar= =2C
Dharmendra Institute of Technology=2C
India.
= --_7ae486e1-db18-44db-a9a2-6528e437d248_-- From owner-chemistry@ccl.net Tue Dec 6 15:48:00 2011 From: "Venable, Richard (NIH/NHLBI) E venabler]-[nhlbi.nih.gov" To: CCL Subject: CCL: MD Simulations Message-Id: <-45997-111206143412-17797-EEHYao/OGjctcXuO9i3fkQ,,server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 6 Dec 2011 14:32:31 -0500 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler^-^nhlbi.nih.gov] Both are good books, although the Frenkel & Smit book seemed biased towards Monte Carlo sampling, at the expense of the MD coverage. Most tutorials are fairly program specific, so you may need to choose a program first. Besides the already mentioned NAMD, you might also look at the LAMMPS, which also available at no cost. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov > From: "Barry Hardy barry.hardy*o*vtxmail.ch" > Reply-To: CCL Subscribers > Date: Tue, 6 Dec 2011 11:48:47 -0500 To: "Venable, Richard (NIH/NHLBI) [E]" > Subject: CCL: MD Simulations Have a look at the following books: Computer simulation of molecular liquids Allen & Tildesley Clarendon Press, Oxford, 1987 Understanding molecular simulation Frenkel & Smit Academic Press, 1996 Marcel Swart On 06 Dec 2011, at 10:09, Sanjay Bharathwaj computationalchemist/./gmail.com wrote: Dear Sir, I am new to molecular dynamics and i wish to understand it before i can start working on it. In this regard, does anyone can point me to the tutorials on various kinds of MD available and theoretical background. Best regards, Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. =================================== dr. Marcel Swart ICREA Research Professor at Institut de Química Computacional Universitat de Girona Facultat de Ciències Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart|a|icrea.cat marcel.swart|a|udg.edu web http://www.marcelswart.eu =================================== From owner-chemistry@ccl.net Tue Dec 6 16:22:00 2011 From: "Sanjay Bharathwaj computationalchemist-.-gmail.com" To: CCL Subject: CCL: MD Simulations Message-Id: <-45998-111206154645-11875-xeKoIW08isw4SDPfqy+0EQ[*]server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=bcaec520f6f7103a7004b37288d6 Date: Tue, 6 Dec 2011 21:46:37 +0100 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist(-)gmail.com] --bcaec520f6f7103a7004b37288d6 Content-Type: text/plain; charset=ISO-8859-1 Dear All, Many thanks for the response. What i am looking for is to carry out a systematic study on the materials using VASP. May be a short introduction of what is the difference between ab-inito MD and a CPMD, and how to decide which one to choose for a particular system would be great. Also, if you have any tutorials for VASP/CASTEP on handling these simulations for a surfaces with a molecule on it would be really helpful. Does any one have this. Best regards, Sanjay On 6 December 2011 17:09, Sanjay Bharathwaj computationalchemist/./gmail.com wrote: > > Dear Sir, > > I am new to molecular dynamics and > i wish to understand it before i can start working on it. > > In this regard, does anyone can point me to the > tutorials on various kinds of MD available and > theoretical background. > > Best regards, > Sanjay > > > > -- > Regards, > Dr. Sanjay Bharathwaj Kumar, > Dharmendra Institute of Technology, > India. > -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, India. --bcaec520f6f7103a7004b37288d6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

Many thanks for the response.

What i am looking for is to carry out
a systematic study= on the materials using VASP.

May be a short intro= duction of what is the difference between
ab-inito MD and a CPMD, and how to decide which one
to choos= e for a particular system would be great.

Also, if= you have any tutorials for VASP/CASTEP
on handling these simulat= ions for a surfaces with a molecule
on it would be really helpful.=A0

Does any on= e have this.

Best regards,
Sanjay
<= div>
On 6 December 2011 17:09, San= jay Bharathwaj computationalchemist/./gmail.co= m <owne= r-chemistry~~ccl.net> wrote:

Dear Sir,<= div>
I am new to molecular dynamics and=A0
i wish to unders= tand it before i can start working on it.

In this = regard, does anyone can point me to the
tutorials on various kind= s of MD available and=A0
theoretical background.=A0

Best regards,
Sanjay



=
--
Regards,
Dr. Sanjay Bh= arathwaj Kumar,
Dharmendra Institute of Technology,
India.



--
Regar= ds,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Technology,<= br>India.
--bcaec520f6f7103a7004b37288d6-- From owner-chemistry@ccl.net Tue Dec 6 16:58:00 2011 From: "ABHISHEK SHAHI shahi.abhishek1984|-|gmail.com" To: CCL Subject: CCL: citation style Message-Id: <-45999-111206153234-708-PJAWtyAU9It1tkWpbfaBHA]=[server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=001636418933496cdc04b372550b Date: Wed, 7 Dec 2011 02:02:04 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984/a\gmail.com] --001636418933496cdc04b372550b Content-Type: text/plain; charset=ISO-8859-1 Dear CCL members, This question regards to citation style. I'm about to finish a paper for a journal (Journal of Molecular structure:theochem).As you know it is painful to write 50 or more references manually and manage them. I am mendeley user but this citation style is not there in mendeley repo ( use .csl extension). I have the citation style for Endnote (.ens extension). So need a help to write my citation in above journal format. Please suggest the easiest way. Is there any way to convert the .ens to .csl or any valuable suggestion from your side. I will be grateful to you. Thank you. **************************************************** *ABHISHEK SHAHI* *Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12* E-mail: shahi++ipc.iisc.ernet.in shahi.abhishek1984++gmail.com * * ***************************************************** --001636418933496cdc04b372550b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL members,=A0

=A0 =A0 =A0 This question regards t= o citation style. I'm about to finish a paper for a journal (Journal of= Molecular=A0structure:theochem).As you know it is painful to write 50 or m= ore references=A0manually and manage them. I am mendeley user but this cita= tion style is not there in mendeley repo ( use .csl extension). I have the = citation style=A0for Endnote (.ens extension). So need a help to write my c= itation in above journal=A0format. Please suggest the easiest way. Is there= =A0any way to convert the .ens to .csl or any valuable suggestion from you= r side. I will be=A0grateful=A0to you. Thank you.


<= br>************************************************= ****

=A0ABHISHEK SHAHI=

Research ScholarInorganic= and Physical Chemistry
In= dian Institute Of Science
Bangalore-12
E-mail: =A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 shahi++ipc.iisc.ernet.in
=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 shahi.abhishek1984++gmail.com


 ***************************************************= **

--001636418933496cdc04b372550b-- From owner-chemistry@ccl.net Tue Dec 6 21:02:01 2011 From: "Dr. Lars Goerigk lars.goerigk/a\chem.usyd.edu.au" To: CCL Subject: CCL: wb97XD in g09 Message-Id: <-46000-111206182526-9657-1ClQb8qIXk3bzTxxvhHrzQ:+:server.ccl.net> X-Original-From: "Dr. Lars Goerigk" Content-Type: multipart/alternative; boundary="------------040605020706080008020003" Date: Wed, 07 Dec 2011 10:25:09 +1100 MIME-Version: 1.0 Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk||chem.usyd.edu.au] This is a multi-part message in MIME format. --------------040605020706080008020003 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hello, I just want to comment, that the 3/124 IOp-switches, that Tobias mentioned, do not work in G09 Rev. A02. So you would need a newer revision or you would have to change the code, if you have it available. Cheers and good luck, Lars -- Dr. Lars Goerigk School of Chemistry (Building F11) The University of Sydney, NSW 2006 Australia --------------040605020706080008020003 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello,
I just want to comment, that the 3/124 IOp-switches, that Tobias mentioned, do not work in G09 Rev. A02. So you would need a newer revision or you would have to change the code, if you have it available.

Cheers and good luck,
Lars

--
Dr. Lars Goerigk
School of Chemistry (Building F11)
The University of Sydney, NSW 2006
Australia
--------------040605020706080008020003--