From owner-chemistry@ccl.net Tue Aug 2 05:48:00 2011 From: "Saman Mandegar mandegar_saman]=[yahoo.com" To: CCL Subject: CCL: Spectra Convolution Message-Id: <-45190-110802054251-14120-02XGakngUpeqJVq6Dq0qRA:+:server.ccl.net> X-Original-From: "Saman Mandegar" Date: Tue, 2 Aug 2011 05:42:47 -0400 Sent to CCL by: "Saman Mandegar" [mandegar_saman : yahoo.com] Dear All, I want to covoulte a vibronic stick spectra with Guassian and Lorentizan distribution functions. I am not pretty sure the algorithm I am using for this work is correct. I would appreciate if any body could guide me in this regard. Best wishes, Saman From owner-chemistry@ccl.net Tue Aug 2 08:04:00 2011 From: "David A Mannock dmannock!=!ualberta.ca" To: CCL Subject: CCL: Reg: Configuration of a group of computers for Speeding up calculations Message-Id: <-45191-110801032127-15303-xO0k5m/3CknINWK+Neqa5g.@.server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=20cf307ac777470a6e04a96c7a88 Date: Mon, 1 Aug 2011 01:21:19 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock(-)ualberta.ca] --20cf307ac777470a6e04a96c7a88 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Rocky, Just another follow up. You can buy cheap 2 or 4 cpu 1207 socket boards that will take 3rd and 4th generation 2000 or 8000 Opteron cpus. The NOS Arima (41-CMGO-D01G) board is on sale at Ebay (item# 110585626008), as are used 2 cpu Supermicro boards ( http://www.supermicro.com/Aplus/motherboard/Opteron2000/MCP55/H8DME-2.cfm) complete with 2x2218 and fans. With 4 or 6 core cpus from Starmicro and cheaper DDR2 memory (2GB/core) you could assemble a 12 -16 core AMD Opteron linux box for ~ $1500. These 12x13" or 13x16" mobos require a large case (Thermaltake Xaser VI VG4000SNA* * or Xigmatek Elysium CCC-HSA0DS-U01), a good power supply (min 850W Corsai= r or Antec. Make sure you have enough connectors), the usual monitor, keyboar= d and mouse or a USB KVM switch (another $500). Use the MX4 CPU gel to attach the fans, not the conductive metal pastes. There are several builds online by computer builders using the Tyan, Asus and Arima boards ( http://www.xtremesystems.org/forums/showthread.php?258619-How-to-Arima-AMD-= Opteron-Quad-Core-Socket-F-3000-series). Google these things first and you will see the problems and the fixes, as well as finding the best price for recommended cases, PSs and memory online= . The lowest price for a 4 cpu system build on the Arima forum was $500. These systems are much more challenging to assemble and set up than a desktop. *Always disconnect the power cable on adding or removing parts fro= m the mobo.* You may need to set up the system with 1 cpu and 1 memory stick first. Some boards require a bios flash or a new bios chip ($10-20) and to do the latter, you may need a dual core cpu (very cheap now) to do this. 2000 series chips are for 2 cpu mobos, whereas 8000 series chips are for 4+ cpu mobos, but can also be used in 2 cpu boards. This should give you a goo= d starting point. But, if you wanted to buy 10 of the above Supermicro boards ||$59 + S&H each, you could have your 40-core cluster and only need to buy a few modular P/Ss and enough A/C to dissipate 10 x 400 watts through a hole in your bedroom wall! lol Excuse the humour! Dave On Tue, Jul 26, 2011 at 12:44 PM, Jussi Lehtola jussi.lehtola*o*helsinki.fi wrote: > > Sent to CCL by: Jussi Lehtola [jussi.lehtola * helsinki.fi] > On Tue, 26 Jul 2011 23:19:46 +0530 > "rocky walden rocky.walden19-.-gmail.com" > wrote: > > Dear CCL folks, > > > > I have 3 Laptop machines which operate 24X7 , so i am planning to > > group them together and try to make a small group so that i can use > > them for exhaustive calculations. > > > > My lappy configuration. > > Intel Dualcore 1.86 GHz,160GB HDD,1GB RAM > > Intel Corei7, (quad core) 1.60Ghz, 6GB RAM, 650 GBHDD, 1 GB Graphics > > ATI Mobil radon > > Intel Corei5 4GB RAM 350GB,HDD, 512 ATI Radon. > > > > All these lappys have windows 7 Ultimate OS > > > > I have license versions of various computational chemistry > > (DESMOND,GROMACS, ABINTIO, )suites, can i set up a home cluster ? > > Can any one give me some ideas > > You are running Windows 7, which is AFAIK unusable for cluster > operation. Basically you could use some of the ready-made cluster linux > distros that run from a CD, but there's really no sense in trying to set > up a cluster with this kind of heterogeneous hardware, especially with a > very slow interconnect (probably 100 MB ethernet). > > You'll be any way restricted to running trivially parallel > calculations. The best you can do is just run separate calculations on > each computer (and maybe install some OS that is more capable for > scientific computing)... > -- > -------------------------------------------------------- > Mr. Jussi Lehtola, M. Sc. Doctoral Student > jussi.lehtola_._helsinki.fi Department of Physics > http://www.helsinki.fi/~jzlehtol University of Helsinki > Office phone: +358 9 191 50 632 Finland > -------------------------------------------------------- > Jussi Lehtola, FM Tohtorikoulutettava > jussi.lehtola_._helsinki.fi Fysiikan laitos > http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto > Ty=F6puhelin: (0)9 191 50 632 > -------------------------------------------------------- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --20cf307ac777470a6e04a96c7a88 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Rocky, Just another follow up. You can buy cheap 2 or 4 cpu 1207 socket boa= rds that will take 3rd and 4th generation 2000 or 8000 Opteron cpus. The NO= S Arima (41-CMGO-D01G) board is on sale at Ebay (item# 110585626008), as ar= e used 2 cpu Supermicro boards (http://www.supermicro.com/Aplus/= motherboard/Opteron2000/MCP55/H8DME-2.cfm) complete with 2x2218 and fan= s. With 4 or 6 core cpus from Starmicro and cheaper DDR2 memory (2GB/core) = you could assemble a 12 -16 core AMD Opteron linux box for ~ $1500. These 1= 2x13" or 13x16" mobos require a large case (Thermaltake Xaser VI = VG4000SNA or Xigmatek Elysium CCC-HSA0DS-U01), a good power supply (min 850W C= orsair or Antec. Make sure you have enough connectors), the usual monitor, = keyboard and mouse or a USB KVM switch (another $500). Use the MX4 CPU gel = to attach the fans, not the conductive metal pastes. There are several buil= ds online by computer builders using the Tyan, Asus and Arima boards (http://www.xtremesystems.org/= forums/showthread.php?258619-How-to-Arima-AMD-Opteron-Quad-Core-Socket-F-30= 00-series). Google these things first and you will see the problems and= the fixes, as well as finding the best price for recommended cases, PSs an= d memory online. The lowest price for a 4 cpu system build on the Arima for= um was $500.

These systems are much more challenging to assemble and set up than a d= esktop. Always disconnect the power cable on adding or removing parts fr= om the mobo. You may need to set up the system with 1 cpu and 1 memory = stick first. Some boards require a bios flash or a new bios chip ($10-20) a= nd to do the latter, you may need a dual core cpu (very cheap now) to do th= is. 2000 series chips are for 2 cpu mobos, whereas 8000 series chips are fo= r 4+ cpu mobos, but can also be used in 2 cpu boards. This should give you = a good starting point. But, if you wanted to buy 10 of the above Supermicro= boards ||$59 + S&H each, you could have your 40-core cluster and only n= eed to buy a few modular P/Ss and enough A/C to dissipate 10 x 400 watts th= rough a hole in your bedroom wall! lol Excuse the humour! Dave

On Tue, Jul 26, 2011 at 12:44 PM, Jussi Leht= ola jussi.lehtola*o*helsinki.fi <owner-chemistry||cc= l.net> wrote:

Sent to CCL by: Jussi Lehtola [jussi.lehtola * helsinki.fi]
On Tue, 26 Jul 2011 23:19:46 +0530
"rocky walden rocky.walden19-.-gmail.com" <owner-chemistry_._ccl.net>
wrote:
> Dear CCL folks,
>
> =A0 =A0 I have 3 Laptop machines which operate 24X7 , so i am planning= to
> group them together and try to make a small group so that i can use > them for exhaustive calculations.
>
> My lappy configuration.
> Intel Dualcore 1.86 GHz,160GB HDD,1GB RAM
> Intel Corei7, (quad core) 1.60Ghz, 6GB RAM, 650 GBHDD, 1 GB =A0Graphic= s
> ATI Mobil radon
> Intel Corei5 =A04GB RAM 350GB,HDD, 512 ATI Radon.
>
> All these lappys have windows 7 Ultimate OS
>
> I have license versions of various computational chemistry
> (DESMOND,GROMACS, ABINTIO, )suites, can i set up a home cluster ?
> Can any one give me some ideas

You are running Windows 7, which is AFAIK unusable for cluster
operation. Basically you could use some of the ready-made cluster linux
distros that run from a CD, but there's really no sense in trying to se= t
up a cluster with this kind of heterogeneous hardware, especially with a very slow interconnect (probably 100 MB ethernet).

You'll be any way restricted to running trivially parallel
calculations. The best you can do is just run separate calculations on
each computer (and maybe install some OS that is more capable for
scientific computing)...
--
--------------------------------------------------------
Mr. Jussi Lehtola, M. Sc. =A0 =A0 =A0 =A0 Doctoral Student
jussi.lehtola_._helsinki.f= i =A0 =A0 =A0 =A0 Department of Physics
http://www= .helsinki.fi/~jzlehtol =A0University of Helsinki
Office phone: +358 9 191 50 632 =A0 Finland
--------------------------------------------------------
Jussi Lehtola, FM =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Tohtorikoulutettava
jussi.lehtola_._helsinki.f= i =A0 =A0 =A0 =A0 Fysiikan laitos
http://www= .helsinki.fi/~jzlehtol =A0Helsingin Yliopisto
Ty=F6puhelin: (0)9 191 50 632
--------------------------------------------------------



-=3D This is automatically added to each message by the mailing script =3D-=
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--20cf307ac777470a6e04a96c7a88-- From owner-chemistry@ccl.net Tue Aug 2 08:39:00 2011 From: "Ravi Kumar Venkatraman ravi.ipc.iisc*gmail.com" To: CCL Subject: CCL: 3 layer ONIOM NMR calculations in G03 Message-Id: <-45192-110802052121-29348-UREJTdP+emxyfK6IDhvQ+w#server.ccl.net> X-Original-From: Ravi Kumar Venkatraman Content-Type: multipart/alternative; boundary=90e6ba53a254f6a81e04a982445f Date: Tue, 2 Aug 2011 14:51:14 +0530 MIME-Version: 1.0 Sent to CCL by: Ravi Kumar Venkatraman [ravi.ipc.iisc:gmail.com] --90e6ba53a254f6a81e04a982445f Content-Type: text/plain; charset=ISO-8859-1 Dear all, Can anybody send me a detailed description about installation of g09 in ubuntu 10.04. Thank you *With Regards,** * * * *Ravi Kumar Venkatraman,* *c/o Prof. Siva Umapathy,** * *IPC Dept., IISc.,* *Bangalore, INDIA.* *Phone No: +91-9686933963* --90e6ba53a254f6a81e04a982445f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Can anybody send me a detail= ed description about installation of g09 in ubuntu 10.04.

Thank you<= br>
With Regards,

Ravi Kumar Venkatraman,
c/o Prof. Siva Umapathy,
IPC Dept., IIS= c.,
Bangalore, INDIA.
Phone No: +91-96869= 33963

--90e6ba53a254f6a81e04a982445f-- From owner-chemistry@ccl.net Tue Aug 2 09:14:00 2011 From: "Gkourmpis, Thomas Thomas.Gkourmpis _ borealisgroup.com" To: CCL Subject: CCL:G: 3 layer ONIOM NMR calculations in G03 Message-Id: <-45193-110802015102-26477-ubKBCpHyTvdU1vpIxYHHBA+*+server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 2 Aug 2011 07:50:48 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis^^borealisgroup.com] Joshi Hi Here you will find all the information you need http://www.gaussian.com/g_tech/g_ur/k_oniom.htm the basic usage of the keywords hasn't change that much from 03 to 09. Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com|a|ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com|a|ccl.net] On Behalf Of krati joshi kjjulie.joshi*|*gmail.com Sent: Monday, August 01, 2011 5:32 PM To: Gkourmpis, Thomas Subject: CCL:G: 3 layer ONIOM NMR calculations in G03 Sent to CCL by: "krati joshi" [kjjulie.joshi##gmail.com] Dear all, I want to do a 3 layer ONIOM NMR calculation using G03 program but i dont know the right keywords for it so if anybody knows pls suggest me the right keywords for it. It will be helpfull. Thanks in advance. Regards Krati Joshi Catalysis Division,NCL Dr. Homi Bhabha road, Pune(Maharashtra) India. Email, Kjjulie.joshi-at-gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose. From owner-chemistry@ccl.net Tue Aug 2 09:48:00 2011 From: "Goncalo Justino jgcj . fct.unl.pt" To: CCL Subject: CCL: mopac and mozype jobs with metal Message-Id: <-45194-110802094543-14724-U+SVJjY7jCqa4B1UKx5tBw : server.ccl.net> X-Original-From: "Goncalo Justino" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 2 Aug 2011 14:45:31 +0100 (WEST) MIME-Version: 1.0 Sent to CCL by: "Goncalo Justino" [jgcj^-^fct.unl.pt] Dear all, I'm trying to do some jobs using MOZYME on a protein that contains a Fe(III) atom. The output of a 0scf indicates that the formal oxidation state of Fe is +2. In agreement with this, a job specifying a doublet state, arising from the Fe(III) atom 2-filled and 1-semi-filled orbitals, fails to run with a "DOUBLET SPECIFIED WITH EVEN NUMBER OF ELECTRONS, CORRECT FAULT". I've been playing around with most of mopac keywords [including metal=(Fe), various cvb and setpi options], but still fail to force it to recognize Fe as Fe(III). Does anyone have any suggestion or comment on this ? All the best, Gonçalo From owner-chemistry@ccl.net Tue Aug 2 10:23:00 2011 From: "Goncalo Justino jgcj_+_fct.unl.pt" To: CCL Subject: CCL: mopac and mozype jobs with metal Message-Id: <-45195-110802101609-13718-mvqMLjMh3OyXTz5eojmBRg[-]server.ccl.net> X-Original-From: "Goncalo Justino" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 2 Aug 2011 15:15:59 +0100 (WEST) MIME-Version: 1.0 Sent to CCL by: "Goncalo Justino" [jgcj()fct.unl.pt] oops... please forget my previous mail... mozyme does not deal with radicals, as per the manual which i should re-read more often... sorry for any waste of time, Gonçalo On Tue, August 2, 2011 14:45, Goncalo Justino wrote: > Dear all, > > I'm trying to do some jobs using MOZYME on a protein that contains a > Fe(III) atom. > > The output of a 0scf indicates that the formal oxidation state of Fe is > +2. In agreement with this, a job specifying a doublet state, arising from > the Fe(III) atom 2-filled and 1-semi-filled orbitals, fails to run with a > "DOUBLET SPECIFIED WITH EVEN NUMBER OF ELECTRONS, CORRECT FAULT". > > I've been playing around with most of mopac keywords [including > metal=(Fe), various cvb and setpi options], but still fail to force it to > recognize Fe as Fe(III). > > Does anyone have any suggestion or comment on this ? > > All the best, > Gonçalo > > From owner-chemistry@ccl.net Tue Aug 2 10:59:00 2011 From: "Herbert Fruchtl herbert.fruchtl_._st-andrews.ac.uk" To: CCL Subject: CCL: mopac and mozype jobs with metal Message-Id: <-45196-110802104753-3381-xjzmDL7/S1jO0TH0++ZsCA_-_server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Aug 2011 15:47:35 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl]![st-andrews.ac.uk] Hi Goncalo, Good to hear from you. I haven't used MOPAC for a while, but I think the error message means that you are trying to get a doublet with an even number of electrons. If your overall charge is not 0, you have to specify it (with the CHARGE keyword). Cheers, Herbert On 08/02/2011 02:45 PM, Goncalo Justino jgcj . fct.unl.pt wrote: > > Sent to CCL by: "Goncalo Justino" [jgcj^-^fct.unl.pt] > Dear all, > > I'm trying to do some jobs using MOZYME on a protein that contains a > Fe(III) atom. > > The output of a 0scf indicates that the formal oxidation state of Fe is > +2. In agreement with this, a job specifying a doublet state, arising from > the Fe(III) atom 2-filled and 1-semi-filled orbitals, fails to run with a > "DOUBLET SPECIFIED WITH EVEN NUMBER OF ELECTRONS, CORRECT FAULT". > > I've been playing around with most of mopac keywords [including > metal=(Fe), various cvb and setpi options], but still fail to force it to > recognize Fe as Fe(III). > > Does anyone have any suggestion or comment on this ? > > All the best, > Gonçalo> > -- 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 Tue Aug 2 14:05:00 2011 From: "Mark Iron mark.a.iron a weizmann.ac.il" To: CCL Subject: CCL: mopac and mozype jobs with metal Message-Id: <-45197-110802112026-5205-q9T5DuWlKz+n4+JMrthcYg]*[server.ccl.net> X-Original-From: Mark Iron Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 2 Aug 2011 18:20:04 +0300 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Mark Iron [mark.a.iron{}weizmann.ac.il] Gonçalo I guess that you decided the the Fe as determined by MOZYME to be Fe(II) based in the partial atomic charge. Remember, that the definition of Fe(III)/Fe(II) in an enzyme (or any other metal-organic system) is a formality based on the ligands bound to it. With the type of ligands prevalent in enzymes, it is not unexpected to find partial atomic charges significantly less than the formal metal oxidation state. Remember that atomic charge and formal oxidation state are not physical observables but rather tools/aids we use to help us understand the observed chemistry. In your case, the formal +3 charge on Fe will be reduced by electron donation from the ligands thus reducing the calculated partial atomic charge on the Fe centre. Changing the spin state from either a singlet or a triplet (as I guess was your initial multiplicity) to a doublet WITHOUT changing (by one unit) the total charge of the system will result in an error similar to that you obtained: with an even number of electrons, one cannot under any circumstances have a doublet spin state (or a quartet or a sextet...). While MOZYME may have problems with a radical system, this is not the error message that you are getting. Hope this helps, Mark. ----------------------------------------------------- Dr. Mark Iron, Computational Chemistry Unit, Department of Chemical Research Support, Kimmelman 251, Weizmann Institute of Science, Rehovot, Israel 76100. Tel: +972 8 934 6218 Fax: +972 8 934 4142 e-mail: mark.a.iron*o*weizmann.ac.il web: http://compchem.weizmann.ac.il/ccu/ No trees were killed in the sending of this message. However, a large number of electrons were terribly inconvenienced. On Aug 2, 2011, at 5:15 PM, Goncalo Justino jgcj_+_fct.unl.pt wrote: > > Sent to CCL by: "Goncalo Justino" [jgcj()fct.unl.pt] > > > oops... > please forget my previous mail... mozyme does not deal with radicals, as > per the manual which i should re-read more often... > > sorry for any waste of time, > Gonçalo > > On Tue, August 2, 2011 14:45, Goncalo Justino wrote: >> Dear all, >> >> I'm trying to do some jobs using MOZYME on a protein that contains a >> Fe(III) atom. >> >> The output of a 0scf indicates that the formal oxidation state of Fe is >> +2. In agreement with this, a job specifying a doublet state, arising from >> the Fe(III) atom 2-filled and 1-semi-filled orbitals, fails to run with a >> "DOUBLET SPECIFIED WITH EVEN NUMBER OF ELECTRONS, CORRECT FAULT". >> >> I've been playing around with most of mopac keywords [including >> metal=(Fe), various cvb and setpi options], but still fail to force it to >> recognize Fe as Fe(III). >> >> Does anyone have any suggestion or comment on this ? >> >> All the best, >> Gonçalo> > From owner-chemistry@ccl.net Tue Aug 2 14:40:00 2011 From: "D.G. Sprous dsprous||bioleap.com" To: CCL Subject: CCL: POL3 water in Tinker Message-Id: <-45198-110802132345-4926-4b0GUEBGGFzCXxjrSJN4hQ/a\server.ccl.net> X-Original-From: "D.G. Sprous" Date: Tue, 2 Aug 2011 13:23:41 -0400 Sent to CCL by: "D.G. Sprous" [dsprous:+:bioleap.com] Dear All: I am attempting to use the POL3 water model in Tinker. I have built a 216mer water box and have attempted to minimize but I keep running into the following error message: INDUCE -- Warning, Induced Dipoles are not Converged TINKER is Unable to Continue; Terminating the Current Calculation I backed out of this and attempted to minimize the simple dimer included in the examples directory which led to the same error. Does anyone have experience/scripts for the proper use of the Tinker program for a simple water box optimization. -- Den