Dear Colle= agues,

I carried out some theoretical calculations o= n complexation of some transition metal ions with a polypyridine ligand and= I predicted the equilibrium constants for the assumed reversible reactions= . I got values of K as high as 1 x 10^400 and in fact, an infinite value in= one case.What do you think about these large values? I interpretated them = to mean that the reactions are essentially irreversible.

<= span>Thank you all.

Olasunkanmi Lukman Olawale<= br>

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Nigeria= .

+234-0-80-52401564 Or +234-0= -80-67161091

--542325855-546353906-1336070535=:64187-- From owner-chemistry@ccl.net Thu May 3 15:21:00 2012 From: "John Keller jwkeller~~alaska.edu" To: CCL Subject: CCL: Tinker Force Field Explorer - installation Message-Id: <-46843-120503150451-22583-qpCFFO4+pPwQSr7c/eeRQg!^!server.ccl.net> X-Original-From: "John Keller" Date: Thu, 3 May 2012 15:04:39 -0400 Sent to CCL by: "John Keller" [jwkeller__alaska.edu] Where are the installation files for the Tinker Force Field Explorer (FFE) program? I cannot see them on the Tinker website. From owner-chemistry@ccl.net Thu May 3 15:56:00 2012 From: "Andrew Yeung andrew.yeung]=[chem.tamu.edu" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46844-120503154350-2953-0iJJwONwauzqU8L0Cs57tw]_[server.ccl.net> X-Original-From: Andrew Yeung Content-Type: multipart/alternative; boundary="------------050907060602080509020301" Date: Thu, 03 May 2012 14:43:29 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung-$-chem.tamu.edu] This is a multi-part message in MIME format. --------------050907060602080509020301 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit How did you do the calculation? Did you find the differences in free energy between the two species, and apply Delta G = - RT ln K? Or is your program able to give you equilibrium constants directly? Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-05-03 1:42 PM, Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk wrote: > Dear Colleagues, > I carried out some theoretical calculations on complexation of some > transition metal ions with a polypyridine ligand and I predicted the > equilibrium constants for the assumed reversible reactions. I got > values of K as high as 1 x 10^400 and in fact, an infinite value in > one case.What do you think about these large values? I interpretated > them to mean that the reactions are essentially irreversible. > Thank you all. > Olasunkanmi Lukman Olawale > ------------------------------------------------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------------------------------------------------ --------------050907060602080509020301 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit How did you do the calculation? Did you find the differences in free energy between the two species, and apply Delta G = - RT ln K?

Or is your program able to give you equilibrium constants directly?

Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837

On 2012-05-03 1:42 PM, Olasunkanmi Lukman Olawale walecomuk^_^yahoo.co.uk wrote:

Dear Colleagues,

I carried out some theoretical calculations on complexation of some transition metal ions with a polypyridine ligand and I predicted the equilibrium constants for the assumed reversible reactions. I got values of K as high as 1 x 10^400 and in fact, an infinite value in one case.What do you think about these large values? I interpretated them to mean that the reactions are essentially irreversible.

Thank you all.

Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.

+234-0-80-52401564 Or +234-0-80-67161091

--------------050907060602080509020301-- From owner-chemistry@ccl.net Thu May 3 16:32:01 2012 From: "Julien C Thibault julien.thibault : utah.edu" To: CCL Subject: CCL: Managing and sharing biomolecular simulation data Message-Id: <-46845-120503155100-10334-lKNveFt+aXAj3qX5meW6pA=-=server.ccl.net> X-Original-From: "Julien C Thibault" Date: Thu, 3 May 2012 15:50:58 -0400 Sent to CCL by: "Julien C Thibault" [julien.thibault]![utah.edu] Hi all, Im currently working with the Cheatham Lab at the University of Utah (http://home.chpc.utah.edu/~cheatham/), trying to develop a system that would facilitate biomolecular simulation data management and sharing at the community level. We are now focusing on AMBER data but we plan to extend it to other software and QM calculations. We prepared a survey to find out which data elements are important to index simulation data and allow community-level queries. You can take the survey here (it takes about 4 minutes): http://www.surveymonkey.com/s/FNZLJVT The vision is to eventually make this open source and open access, so your feedback is important. Thanks, Julien Thibault University of Utah Department of Biomedical Informatics 26 South 2000 East Room 5775 HSEB Salt Lake City, UT 84112 julien.thibault%utah.edu From owner-chemistry@ccl.net Thu May 3 17:06:00 2012 From: "cina foroutan canyslopus()yahoo.co.uk" To: CCL Subject: CCL: Large value of equilibrium constants Message-Id: <-46846-120503164810-13813-2XncskCUWmvu6AAUGhs0Jg : server.ccl.net> X-Original-From: cina foroutan Content-Type: multipart/alternative; boundary="-976153366-2033782622-1336078082=:78578" Date: Thu, 3 May 2012 21:48:02 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: cina foroutan [canyslopus{=}yahoo.co.uk] ---976153366-2033782622-1336078082=:78578 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Olasunkanmi,=0A=0AWould you please mention at which theoretical level = you performed the computations. Is it an ab initio or DFT or it is of semi-= empirical/molecular mechanic level? This might be a systematic error due to= the computational level. Would you please also mention the amount of the b= inding energies between the metal and ligands. If the binding energy is ver= y large, you must improve your computational level.=0ASee this reference as= an example of wrong computational level selection: Sensors, 2007, 7, 3119.= =0A=0AGood Luck!=0ACina=0A*************************************************= ***********************************************=0A=0ACina Foroutan-Nejad, P= h.D.=0ASchool of Chemistry, College of Science=0AUniversity of Tehran, Tehr= an, Iran=0Ahttp://independent.academia.edu/CinaForoutanNejad=0A=0A=0A=0A___= _____________________________=0A From: Olasunkanmi Lukman Olawale walecomuk= ^_^yahoo.co.uk =0ATo: "Foroutan-Nejad, Cina -id#47= z-" =0ASent: Thursday, 3 May 2012, 22:42=0ASubject= : CCL: Large value of equilibrium constants=0A =0A=0ADear Colleagues,=0AI c= arried out some theoretical calculations on complexation of some transition= metal ions with a polypyridine ligand and I predicted the equilibrium cons= tants for the assumed reversible reactions. I got values of K as high as 1 = x 10^400 and in fact, an infinite value in one case.What do you think about= these large values? I interpretated them to mean that the reactions are es= sentially irreversible.=0AThank you all.=0A=0A=A0=0AOlasunkanmi Lukman Olaw= ale=0A________________________________=0ACurrent Address:=0ADepartment of C= hemistry,=0AObafemi Awolowo University,=0AIle-Ife, Osun State.=0ANigeria.= =0A=0A+234-0-80-52401564 Or +234-0-80-67161091=0A__________________________= ______ ---976153366-2033782622-1336078082=:78578 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Olasunkanmi,

Would you please mention at= which theoretical level you performed the computations. Is it an ab initio= or DFT or it is of semi-empirical/molecular mechanic level? This might be = a systematic error due to the computational level. Would you please also me= ntion the amount of the binding energies between the metal and ligands. If = the binding energy is very large, you must improve your computational level= .

See this reference as an example of wrong computat= ional level selection: Sensors, 2007, 7, 3119.

<= /span>

Good Luck!

Cina

<= div>*****************************************************************= *******************************

Cina Foroutan-Nejad, Ph.D.

School of Chemistry, College = of Science

University of Tehran, Tehran, Iran=

http://independent.academia.edu/CinaForoutanNejad

From: Olasunkanmi Lukman Olawale walecomuk^_^ya= hoo.co.uk <owner-chemistry_+_ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus_+_yaho= o.co.uk>
Sent: Thu= rsday, 3 May 2012, 22:42
Subject:= CCL: Large value of equilibrium constants

Dear Colleagues,

I carried out some theoretical = calculations on complexation of some transition metal ions with a polypyrid= ine ligand and I predicted the equilibrium constants for the assumed revers= ible reactions. I got values of K as high as 1 x 10^400 and in fact, an inf= inite value in one case.What do you think about these large values? I inter= pretated them to mean that the reactions are essentially irreversible.

Thank you all.

Olasunkanmi Lukman Olaw= ale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile= -Ife, Osun State.
Nigeria.

+234-0-80-52401564 Or +234-0-80-67161091

---976153366-2033782622-1336078082=:78578-- From owner-chemistry@ccl.net Thu May 3 19:53:00 2012 From: "David A Mannock dmannock**ualberta.ca" To: CCL Subject: CCL:G: run parallel G09 without Linda (re-send) Message-Id: <-46847-120503172423-21531-gSEhQ70DW/K6Zx1kT8UIAQ[a]server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=bcaec554de6008d29004bf286d42 Date: Thu, 3 May 2012 15:24:15 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock^ualberta.ca] --bcaec554de6008d29004bf286d42 Content-Type: text/plain; charset=ISO-8859-1 Hi! I am just running an Opt+ Freq calculation in G09. Top shows the most cpu intensive applications on the top line and presently shows 1199% CPU and 90.2% memory in use. This means that the 12 cores on my AMD motherboard and 90% of 7GB (8GB installed) are being used in the calculation. This may be different for Intel CPUs. Occasionally results will be written to disk and those numbers will fall slightly or a subroutine will be called that uses only a single core, this is normal. I believe that G09 may have some limitations above 32 cores. In my new server which contains 64 cores, I have installed 128 GB of memory and online it suggests leaving 4GB free. The rule for onboard memory in smaller systems is: 2* (# cores) - 1GB. Thus, for my present system, I may have to add more DDR2 to the motherboard to improve the calculation efficiency. Dave On Thu, May 3, 2012 at 3:45 AM, uekstrom],[gmail.com uekstrom],[gmail.com < owner-chemistry!^!ccl.net> wrote: > > Sent to CCL by: "uekstrom**gmail.com" [uekstrom**gmail.com] > > After submitted the job, using the top command in the compute-node I > found > > only 1 processor is running with %CPU of several hundreds. And in the log > > file, there was a line "Will use up to 8 processors via shared memory" > > I don't know anything about Gaussian, but it's normal that top > aggregates many threads as one process using > 100% cpu. For example > on my two (physical) core machine I usually have 350% cpu utilization > for a single process, this means that there are about 3.5 threads > running at the same time (presumably using hyper threading). You can > play with arguments to top to see all threads (i.e. -H). > > Regards, > Ulf Ekstrom, University of Oslo> > > --bcaec554de6008d29004bf286d42 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi! I am just running an Opt+ Freq calculation in G09. Top shows the most c= pu intensive applications on the top line and presently shows 1199% CPU and= 90.2% memory in use. This means that the 12 cores on my AMD motherboard an= d 90% of 7GB (8GB installed) are being used in the calculation. This may be= different for Intel CPUs. Occasionally results will be written to disk and= those numbers will fall slightly or a subroutine will be called that uses = only a single core, this is normal. I believe that G09 may have some limita= tions above 32 cores. In my new server which contains 64 cores, I have inst= alled 128 GB of memory and online it suggests leaving 4GB free. The rule fo= r onboard memory in smaller systems is: 2* (# cores) - 1GB. Thus, for my pr= esent system, I may have to add more DDR2 to the motherboard to improve the= calculation efficiency. Dave

On Thu, May 3, 2012 at 3:45 AM, uekstrom],[<= a href=3D"http://gmail.com">gmail.com uekstrom],[gmail.com <owner-chemistry!^!ccl.net> wrote:<= br>

Sent to CCL by: "uekstrom**gmail.com" [uekstrom**gmail.com]
> After submitted the job, using the top command in the compute-node I f= ound
> only 1 processor is running with %CPU of several hundreds. And in the = log
> file, there was a line "Will use up to 8 processors via shared me= mory"

I don't know anything about Gaussian, but it's normal that top
aggregates many threads as one process using > 100% cpu. For example
on my two (physical) core machine I usually have 350% cpu utilization
for a single process, this means that there are about 3.5 threads
running at the same time (presumably using hyper threading). You can
play with arguments to top to see all threads (i.e. -H).

Regards,
Ulf Ekstrom, University of Oslo

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