From owner-chemistry@ccl.net Fri Dec 10 04:48:01 2010 From: "Daniel Jana dfjana~~gmail.com" To: CCL Subject: CCL: Running GAMESS on ROCKS using SGE Message-Id: <-43317-101210044618-23687-ftUXhnqMREizk8CYHFH56Q]=[server.ccl.net> X-Original-From: Daniel Jana Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 10 Dec 2010 10:46:09 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana*_*gmail.com] Hello, Have you tried asking for help in the GridEngine user mailing list? This old email may be a good starting point: http://gridengine.sunsource.net/ds/viewMessage.do?dsForumId=38&dsMessageId=10286 Any questions you may come up with should more easily be discussed there than here. Best of luck, Daniel On 10 December 2010 00:00, rkdelisle^gmail.com wrote: > I'm struggling to get GAMESS to run within a ROCKS cluster using SGE. > Working through the sge-gms and rungms scripts is a very convoluted process. > Has anyone implemented something similar? I'll hold off on further > details/questions until I hear back. > > -Kirk From owner-chemistry@ccl.net Fri Dec 10 07:23:00 2010 From: "Anup Thomas anupiict|gmail.com" To: CCL Subject: CCL: Regarding ELF Plotting Message-Id: <-43318-101210071827-20130-V61husxkRmr2WU+S+BTKFg,,server.ccl.net> X-Original-From: "Anup Thomas" Date: Fri, 10 Dec 2010 07:18:25 -0500 Sent to CCL by: "Anup Thomas" [anupiict**gmail.com] Dear all Could any one explain me some of the input data of ELF generation What we have to give 1) as input the origin of the grid x,y,z 2) nput edges along x,y,z 3) input the number of intervals along x,y,z There are some indicatives so based on these indications how we can give the inputs? is there any particular way to follow. Please (any one help me) Regards Anup From owner-chemistry@ccl.net Fri Dec 10 08:41:00 2010 From: "Gopakumar scschem=gmail.com" To: CCL Subject: CCL: Regarding ELF Plotting Message-Id: <-43319-101210083952-20846-zLrP9BhtLs7d5nt59tzycA###server.ccl.net> X-Original-From: Gopakumar Content-Type: multipart/alternative; boundary=0016e6470e48aac8e804970e7c49 Date: Fri, 10 Dec 2010 14:39:23 +0100 MIME-Version: 1.0 Sent to CCL by: Gopakumar [scschem|a|gmail.com] --0016e6470e48aac8e804970e7c49 Content-Type: text/plain; charset=ISO-8859-1 Hi, I don't know which software you are using to plot ELF. If it is TopMod, there is a small tutorial available at http://www.lct.jussieu.fr/pagesperso/silvi/clark.html Hope it helps -Gopakumar On Fri, Dec 10, 2010 at 1:18 PM, Anup Thomas anupiict|gmail.com < owner-chemistry : ccl.net> wrote: > > Sent to CCL by: "Anup Thomas" [anupiict**gmail.com] > Dear all > > Could any one explain me some of the input data of ELF generation > > What we have to give > > 1) as input the origin of the grid x,y,z > > 2) nput edges along x,y,z > > 3) input the number of intervals along x,y,z > > There are some indicatives so based on these indications how we can give > the inputs? is there any particular way to follow. > > Please (any one help me) > > Regards > Anup> > > --0016e6470e48aac8e804970e7c49 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

=A0=A0 I don't know which software you are using to plot ELF= .
If it is TopMod, there is a small tutorial available at

http://www.lct.j= ussieu.fr/pagesperso/silvi/clark.html

Hope it helps

-Gopakumar





On Fri, Dec 10, 2010 at 1:18 PM, Anup Thomas anupiict|gmail.com <owner-chemistry : ccl.net> wrote:

Sent to CCL by: "Anup =A0Thomas" [anupiict**gmail.com]
Dear all

=A0 Could any one explain me some of the input data of ELF generation

What we have to give

1) as input the origin of the grid x,y,z

2) nput edges along x,y,z

3) input the number of intervals along x,y,z

There are some indicatives so based on these indications how we can give th= e inputs? is there any particular way to follow.

Please (any one help me)

Regards
Anup



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--0016e6470e48aac8e804970e7c49-- From owner-chemistry@ccl.net Fri Dec 10 09:44:00 2010 From: "Eduard Matito ematito]![gmail.com" To: CCL Subject: CCL: Regarding ELF Plotting Message-Id: <-43320-101210085749-22423-7bseb4CzCFHWacxjYYw8lA]-[server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 10 Dec 2010 14:57:37 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eduard Matito [ematito_+_gmail.com] For what you say, I assume you are using ToPMoD program... if not, disregard what comes next. Here you have the manual of topmod: http://www.lct.jussieu.fr/pagesperso/silvi/manual/manual.html The preparation of the inputs can be done automatically using the perl script by Alex Clark: http://www.lct.jussieu.fr/pagesperso/silvi/clark.html You can also use an old f90 simple code I wrote for this purpose, it only needs a txt file (molecule.txt) with the number of atoms in the first line and the Cartesian Coordinates afterwards. Execute like this: ./program molecule.txt it will generate molecule*.inp needed for ToPMoD collection of programs. Hope it helps, Eduard *-------- PROGRAM INPUT_ELF IMPLICIT INTEGER(I-N) IMPLICIT REAL*8(A-H,O-Z) REAL*8, DIMENSION(:,:), ALLOCATABLE :: D REAL*8, DIMENSION(:), ALLOCATABLE :: Aminim,Amaxim,Tamany INTEGER, DIMENSION(:), ALLOCATABLE :: Grid CHARACTER*25 filein,file CHARACTER*80 noth Call GETARG(1,filein) nllarg=len_trim(filein) file=filein(1:nllarg)//".txt" OPEN(unit=12,file=file,status='old') file=filein(1:nllarg)//"_1.inp" OPEN(unit=32,file=file,status='unknown') file=filein(1:nllarg)//"_2.inp" OPEN(unit=42,file=file,status='unknown') file=filein(1:nllarg)//"_2r.inp" OPEN(unit=44,file=file,status='unknown') file=filein(1:nllarg)//"_3.inp" OPEN(unit=52,file=file,status='unknown') read(12,*) Nuclis ALLOCATE(D(Nuclis,3),Aminim(3),Amaxim(3),Tamany(3)) ALLOCATE(Grid(3)) D=0.0d0 do i=1,Nuclis read(12,*) (D(i,j),j=1,3) enddo do j=1,3 Aminim(j)=1000.0d0 Amaxim(j)=-1000.0d0 enddo do i=1,Nuclis do j=1,3 if (D(i,j).lt.Aminim(j)) Aminim(j)=D(i,j) if (D(i,j).gt.Amaxim(j)) Amaxim(j)=D(i,j) enddo enddo do j=1,3 Aminim(j)=Aminim(j)-5 Amaxim(j)=Amaxim(j)+5 Tamany(j)=Amaxim(j)-Aminim(j) Grid(j)=int(Tamany(j)*10) enddo nllarg=len_trim(filein) file=filein(1:nllarg)//".wfn" write(32,'(A25)') file !write(32,'(A1)') 'n' write(32,'(3(f6.2,1X))') (Aminim(j),j=1,3) write(32,'(3(f6.1,1X))') (Tamany(j),j=1,3) write(32,'(3(I3,1X))') (Grid(j),j=1,3) write(42,'(a3)') 'elf' write(42,'(a25)') file write(42,'(a1)') '1' write(42,'(a1)') 'n' write(42,'(a1)') '0' write(42,'(a1)') 'y' write(44,'(a3)') 'rho' write(44,'(a25)') file write(44,'(a1)') '1' write(44,'(a1)') 'y' write(52,'(a25)') file write(52,'(a1)') '7' write(52,'(a3)') '0 0' CLOSE(12) CLOSE(32) CLOSE(42) CLOSE(44) CLOSE(52) END *-------- On Dec 10, 2010, at 1:18 PM, Anup Thomas anupiict|gmail.com wrote: > > Sent to CCL by: "Anup Thomas" [anupiict**gmail.com] > Dear all > > Could any one explain me some of the input data of ELF generation > > What we have to give > > 1) as input the origin of the grid x,y,z > > 2) nput edges along x,y,z > > 3) input the number of intervals along x,y,z > > There are some indicatives so based on these indications how we can > give the inputs? is there any particular way to follow. > > Please (any one help me) > > Regards > Anup > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > -- Eduard Matito Postdoctoral researcher Institute of Physics University of Szczecin Wielkopolska 15 70451 Szczecin (Poland) Phone: +48914441436 http://ematito.webs.com From owner-chemistry@ccl.net Fri Dec 10 10:19:00 2010 From: "Peter D Jarowski p.d.jarowski^^^surrey.ac.uk" To: CCL Subject: CCL: Freeware Molecular Mechanics Message-Id: <-43321-101210094929-8473-wQJL9HWpXDVsGfyOXRfi/w:+:server.ccl.net> X-Original-From: "Peter D Jarowski" Date: Fri, 10 Dec 2010 09:49:28 -0500 Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] Hello, Anyone know of a freeware molecular mechanics package with a reasonable GUI that runs on Mac intel? All I need is to run some preliminary minimizations and/or conformational searches before submitting to the cluster for QM. I know about Tinker, but I do not see a GUI for that one. Best, Peter From owner-chemistry@ccl.net Fri Dec 10 11:15:00 2010 From: "Robert DeLisle rkdelisle*gmail.com" To: CCL Subject: CCL: Running GAMESS on ROCKS using SGE Message-Id: <-43322-101210111338-8409-mDNFcwQC/VKkPqH+CA4kDQ()server.ccl.net> X-Original-From: Robert DeLisle Content-Type: multipart/alternative; boundary=0015175cd0788bed0b049710a267 Date: Fri, 10 Dec 2010 09:13:29 -0700 MIME-Version: 1.0 Sent to CCL by: Robert DeLisle [rkdelisle*gmail.com] --0015175cd0788bed0b049710a267 Content-Type: text/plain; charset=ISO-8859-1 Thank you for the link. That gives me another relevant reference. In looking through it, it does remain a bit cryptic - much like the rungms and sge-gms scrips of GAMESS. Any additional links or clarification would be greatly appreciated. -Kirk On Fri, Dec 10, 2010 at 2:46 AM, Daniel Jana dfjana~~gmail.com < owner-chemistry*ccl.net> wrote: > > Sent to CCL by: Daniel Jana [dfjana*_*gmail.com] > Hello, > > Have you tried asking for help in the GridEngine user mailing list? > This old email may be a good starting point: > > http://gridengine.sunsource.net/ds/viewMessage.do?dsForumId=38&dsMessageId=10286 > > Any questions you may come up with should more easily be discussed > there than here. > > Best of luck, > Daniel > > On 10 December 2010 00:00, rkdelisle^gmail.com > wrote: > > I'm struggling to get GAMESS to run within a ROCKS cluster using SGE. > > Working through the sge-gms and rungms scripts is a very convoluted > process. > > Has anyone implemented something similar? I'll hold off on further > > details/questions until I hear back. > > > > -Kirk> > > --0015175cd0788bed0b049710a267 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you for the link.=A0 That gives me another relevant reference.
In looking through it, it does remain a bit cryptic - much like the rungm= s and sge-gms scrips of GAMESS.=A0 Any additional links or clarification wo= uld be greatly appreciated.

-Kirk





On Fri, Dec 10,= 2010 at 2:46 AM, Daniel Jana dfjana~~gmail.co= m <owne= r-chemistry*ccl.net> wrote:

Sent to CCL by: Daniel Jana [dfjana*_*gmail.com]
Hello,

Have you tried asking for help in the GridEngine user mailing list?
This old email may be a good starting point:
http://gridengine.sunsource.net= /ds/viewMessage.do?dsForumId=3D38&dsMessageId=3D10286

Any questions you may come up with should more easily be discussed
there than here.

Best of luck,
Daniel

On 10 December 2010 00:00, rkdelisle^gmail.com <owner-chemistry]~[ccl.net> wrote:
> I'm struggling to get GAMESS to run within a ROCKS cluster using S= GE.
> Working through the sge-gms and rungms scripts is a very convoluted pr= ocess.
> Has anyone implemented something similar? I'll hold off on further=
> details/questions until I hear back.
>
> -Kirk



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--0015175cd0788bed0b049710a267-- From owner-chemistry@ccl.net Fri Dec 10 12:27:00 2010 From: "Daniel Jana dfjana]^[gmail.com" To: CCL Subject: CCL: Running GAMESS on ROCKS using SGE Message-Id: <-43323-101210122416-10747-ToW7aZkBYRBO6a+hZLMqdQ||server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 10 Dec 2010 18:24:10 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana#gmail.com] Unfortunately I cannot go much beyond that. The only cluster where I had to install GAMESS uses PBS which, in terms of parallel environments is a lot more permissive. SGE is (in my opinion) a nicer queuing system, but (especially for GAMESS) first set up can be a pain. It does not help much the way rungms is done either... in fact, one does better simply stripping off the relevant bits of rungms and making a new script for submitting jobs (that is what the subgms in that email is for). Queuing systems (especially the kind of help you are in need of) go well beyond the scope of this list. Contact me through private email with some specific question and I may be able to help you. Over the weekend I'll try to set GAMESS up on a cluster with SGE and perhaps we can discuss this further. Best, Daniel On 10 December 2010 17:13, Robert DeLisle rkdelisle*gmail.com wrote: > Thank you for the link.  That gives me another relevant reference. > > In looking through it, it does remain a bit cryptic - much like the rungms > and sge-gms scrips of GAMESS.  Any additional links or clarification would > be greatly appreciated. > > -Kirk > From owner-chemistry@ccl.net Fri Dec 10 13:01:00 2010 From: "Toomas Tamm tt-ccl2_-_yki.ttu.ee" To: CCL Subject: CCL: temperature and free rotation Message-Id: <-43324-101210121542-5191-e+yT/sVbQ3f5Rc8jc6k6eg=-=server.ccl.net> X-Original-From: Toomas Tamm Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 10 Dec 2010 19:15:18 +0200 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2~!~yki.ttu.ee] Hello, I have been unable to find a clear answer to the following problem: Suppose we have calculated the energy profile of rotation about a given single bond in a molecule. Given this data, I would like to know if the conformers freely interconvert into each other (ie the molecule can cross the rotational barrier) at a given temperature T. My original thought was to compare the barrier height with the energy available in a vibrational mode, 1/2 kT. However, this leads to the result that most methyl groups (barriers 2-3 kcal/mol) should not rotate at room temperature (1/2 kT x N_A = 1/2 RT = 0.297 kcal/mol at 298K), which contradicts common chemical knowledge. I understand that eventually we get to the kinetics aspect of the problem (how rapid is the interconversion rate of conformers), but I would rather like to have a general "rule of thumb" which could be used for quick estimates. Which value do I need to compare the barrier height with? -- Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Fri Dec 10 13:37:00 2010 From: "P.D.Jarowski:-:surrey.ac.uk" To: CCL Subject: CCL: Mm with metals Message-Id: <-43325-101210123335-20475-21JROXcJaCUQiwFwz0f/EA\a/server.ccl.net> X-Original-From: Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC6EXMB01CMSsurr_" Date: Fri, 10 Dec 2010 17:31:57 +0000 MIME-Version: 1.0 Sent to CCL by: [P.D.Jarowski]=[surrey.ac.uk] --_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC6EXMB01CMSsurr_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGksIEkgYW0gbG9va2luZyB0byBkbyBzb21lIGNvbmZvcm1hdGlvbiBzZWFyY2hpbmcgb24gc29t ZSBsYXJnZSBzeXN0ZW1zIGludm9sdmluZyBzcXVhcmUgcGxhbmFyIG1ldGFsIGNlbnRlcnMgd2l0 aCBvcmdhbmljIGxpZ2FuZHMuIFdoYXQgYXJlIHlvdXIgdGhvdWdodHMgb24gdGhlIGF2YWlsYWJs ZSBmZnMgZm9yIG1ldGFscyBhbmQgd2hhdCBwcm9ncmFtcyBhcmUgYXZhaWxhYmxlIHRvIGltcGxl bW1lbnQgdGhlbT8NCg0KQWdhaW4sIEkgYW0gYWx3YXlzIGxvb2tpbmcgZm9yIGZyZWV3YXJlLCBi dXQgb3RoZXJzIHdvdWxkIGJlIGFwcHJlY2lhdGVkIHRvby4gVGhhbmtzLA0KDQpQZXRlcg0KDQoq KipTZW50IHZpYSBSb2FkU3luY8KuIGZvciBBbmRyb2lk4oSiDQo= --_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC6EXMB01CMSsurr_ Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 PHNwYW4gc3R5bGU9ImZvbnQtc2l6ZToxMS4wcHQ7IGZvbnQtZmFtaWx5OiZxdW90O0NhbGlicmkm cXVvdDssJnF1b3Q7c2Fucy1zZXJpZiZxdW90OyI+SGksIEkgYW0gbG9va2luZyB0byBkbyBzb21l IGNvbmZvcm1hdGlvbiBzZWFyY2hpbmcgb24gc29tZSBsYXJnZSBzeXN0ZW1zIGludm9sdmluZyBz cXVhcmUgcGxhbmFyIG1ldGFsIGNlbnRlcnMgd2l0aCBvcmdhbmljIGxpZ2FuZHMuIFdoYXQgYXJl IHlvdXIgdGhvdWdodHMgb24gdGhlIGF2YWlsYWJsZSBmZnMgZm9yIG1ldGFscyBhbmQgd2hhdCBw cm9ncmFtcyBhcmUgYXZhaWxhYmxlIHRvIGltcGxlbW1lbnQgdGhlbT88YnI+PGJyPkFnYWluLCBJ IGFtIGFsd2F5cyBsb29raW5nIGZvciBmcmVld2FyZSwgYnV0IG90aGVycyB3b3VsZCBiZSBhcHBy ZWNpYXRlZCB0b28uIFRoYW5rcyw8YnI+PGJyPlBldGVyPGJyPjxicj4qKipTZW50IHZpYSBSb2Fk U3luY8KuIGZvciBBbmRyb2lk4oSiPC9zcGFuPg0K --_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC6EXMB01CMSsurr_-- From owner-chemistry@ccl.net Fri Dec 10 14:12:00 2010 From: "Jason Swails swails- -qtp.ufl.edu" To: CCL Subject: CCL: Freeware Molecular Mechanics Message-Id: <-43326-101210124829-3319-hfN7HZ/8nwubscc8pMREtA|,|server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=00151748db4cd05a26049711f54b Date: Fri, 10 Dec 2010 12:48:21 -0500 MIME-Version: 1.0 Sent to CCL by: Jason Swails [swails+*+qtp.ufl.edu] --00151748db4cd05a26049711f54b Content-Type: text/plain; charset=ISO-8859-1 Gabedit is *reasonably* easy to compile on a Mac (they have detailed enough instructions). This interfaces (via GUI) with a number of quantum mechanical packages. VMD is another decent option, and it interfaces with namd (both are free). Good luck! Jason On Fri, Dec 10, 2010 at 9:49 AM, Peter D Jarowski p.d.jarowski^^^ surrey.ac.uk wrote: > > Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] > Hello, > > Anyone know of a freeware molecular mechanics package with a reasonable GUI > that runs on Mac > intel? All I need is to run some preliminary minimizations and/or > conformational searches before > submitting to the cluster for QM. I know about Tinker, but I do not see a > GUI for that one. > > Best, > > Peter> > > -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --00151748db4cd05a26049711f54b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Gabedit is *reasonably* easy to compile on a Mac (they have detailed enough= instructions).=A0 This interfaces (via GUI) with a number of quantum mecha= nical packages.

VMD is another decent option, and it interfaces with= namd (both are free).

Good luck!
Jason

On Fri, Dec 10, 2= 010 at 9:49 AM, Peter D Jarowski p.d.jarowski^^^surrey.ac.uk <owner-chemistry#,#ccl.net> wrote:

Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk]
Hello,

Anyone know of a freeware molecular mechanics package with a reasonable GUI= that runs on Mac
intel? All I need is to run some preliminary minimizations and/or conformat= ional searches before
submitting to the cluster for QM. I know about Tinker, but I do not see a G= UI for that one.

Best,

Peter



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--
Jason M. Swails
Quan= tum Theory Project,
University of Florida
Ph.D. Graduate Student
3= 52-392-4032
--00151748db4cd05a26049711f54b-- From owner-chemistry@ccl.net Fri Dec 10 14:47:01 2010 From: "Utpal Sarkar utpalchemiitkgp(0)gmail.com" To: CCL Subject: CCL:G: Help for cluster Message-Id: <-43327-101210123934-29767-r6xiknkCUhEj704ol+uRNA~!~server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: multipart/alternative; boundary=0015175933a2fac335049711d5bd Date: Fri, 10 Dec 2010 23:09:27 +0530 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp.,.gmail.com] --0015175933a2fac335049711d5bd Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sir, we will run specially abinito software like gaussian, vasp etc and also molecular dymanics software like DL_PLOY. Regarding the OS, I can install LINUX, but the application softwares sometimes need to specify specific path of the library files, that I have doubt, since sometimes I face problem regaring this (even sometimes the MAKEFILE also need to be modify as per th= e architechture of the machines, and that sometimes also give lot of pain) We have to maintain the machines ourselves since we don't have any system administer. regards utpal 2010/12/9 Ulf Ekstr=F6m ulfek:+:few.vu.nl > Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek]-[few.vu.nl] > On Wed, Dec 8, 2010 at 5:48 PM, Utpal Sarkar > utpalchemiitkgp[-]gmail.com wrote: > > Dear CCL users, > > We are planning to purchase a 16 node (o= r > > even 32 node depending upon the price needed) cluser in which we will r= un > > softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly > give > > your valuable suggestion about: > > a) which type of specification is better ? > > Exactly what kind of jobs will you run? This is important since it > will tell us how much memory, network bandwidth and disk performance > you need. > > > b) How much does it cost (we can spent upto $10K to $11K) ? > > c) does the company/ provider (ie, HP, Dell, SGI ets) will install the > > cluster in the lab or we have to install ourself? > > They will install an operating system for you if you pay, however the > operating system is usually very easy to install, the applications are > more difficult. > > > We are starting from the begining and have no idel of purchasing > clusters, > > so asking so many questions. > > Will you maintain this machine yourself? Generally if you have a > good/cheap administrator you can buy components of lower quality, and > in some sense get more for your money. You cluster will be so small > that you perhaps won't need a very expensive file server, for example. > However, if you have to pay for maintenance when something breaks you > really should consider some fancier hardware. > > Regards, > Ulf Ekstrom > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --0015175933a2fac335049711d5bd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sir,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 we will run specially abinito softwa= re like gaussian, vasp etc and also molecular dymanics software like DL_PLO= Y.
=A0
Regarding the OS, I can install LINUX, but the application softwares s= ometimes need to specify specific path of the library files, that I have do= ubt, since sometimes I face problem
regaring this (even sometimes the MAKEFILE also need to be modify as p= er the architechture of the machines, and that sometimes also give lot of p= ain)
=A0
We have to maintain the machines ourselves since we don't have any= system administer.
regards
utpal


=A0
2010/12/9 Ulf Ekstr=F6m ulfek:+:few.vu.nl <owner-chemistry,ccl.netftw= are

Sent to CCL by: =3D?ISO-8859= -1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek]-[few.vu.nl]
On Wed, Dec 8, 2010 at 5:48 PM, Utpal Sarkar
utpalchemiitkgp[-]gmail.com <owner-chemistry]= ^[ccl.net> wrote:
&= gt; Dear CCL users,
> =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 We are planning to purchase a 16 node (or
> eve= n 32 node depending upon the price needed) cluser in which we will run
&= gt; softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly = give
> your valuable suggestion about:
> a) which type of specification= is better ?

Exactly what kind of jobs will you run? This is importa= nt since it
will tell us how much memory, network bandwidth and disk per= formance
you need.

> b) How much does it cost (we can spent upto $10K to $= 11K) ?
> c) does the company/ provider (ie, HP, Dell, SGI ets) will i= nstall the
> cluster in the lab or we have to install ourself?

They will install an operating system for you if you pay, however theoperating system is usually very easy to install, the applications aremore difficult.

> We are starting =A0from the begining and have = no idel of purchasing clusters,
> so asking so many questions.

Will you maintain this machine you= rself? Generally if you have a
good/cheap administrator you can buy comp= onents of lower quality, and
in some sense get more for your money. You = cluster will be so small
that you perhaps won't need a very expensive file server, for example.<= br>However, if you have to pay for maintenance when something breaks youreally should consider some fancier hardware.

Regards,
Ulf Ekstr= om



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--0015175933a2fac335049711d5bd-- From owner-chemistry@ccl.net Fri Dec 10 15:22:00 2010 From: "Daniel Jana dfjana..gmail.com" To: CCL Subject: CCL: Freeware Molecular Mechanics Message-Id: <-43328-101210123543-25975-t9c+wMkFtzPS/dQisBe5vw:+:server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 10 Dec 2010 18:35:37 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana^^gmail.com] Not sure it covers all your needs (it does have MM and a nice graphical interface), but this comes to mind: http://avogadro.openmolecules.net/wiki/Main_Page When I last used it it wasn't the most stable package on the planet, but a few versions have come out since... Best regards, Daniel Jana On 10 December 2010 15:49, Peter D Jarowski p.d.jarowski^^^surrey.ac.uk wrote: > > Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] > Hello, > > Anyone know of a freeware molecular mechanics package with a reasonable GUI that runs on Mac > intel? All I need is to run some preliminary minimizations and/or conformational searches before > submitting to the cluster for QM. I know about Tinker, but I do not see a GUI for that one. > > Best, > > Peter>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Fri Dec 10 15:57:01 2010 From: "Mark Mackey Mark||cresset-group.com" To: CCL Subject: CCL: Freeware Molecular Mechanics Message-Id: <-43329-101210130903-6718-pO9F6Lq7aPrkLhLhY2LoDg||server.ccl.net> X-Original-From: "Mark Mackey" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 10 Dec 2010 18:07:37 -0000 MIME-Version: 1.0 Sent to CCL by: "Mark Mackey" [Mark/./cresset-group.com] FieldView (http://www.cresset-group.com/product/fieldview) is free, there's a Mac version, and it will let you minimise molecules. It doesn't have conformation searching capability, though. Mark. -- Dr Mark Mackey Director, Development Cresset Biomolecular Discovery -----Original Message----- > From: owner-chemistry+mark==cresset-bmd.com-*-ccl.net [mailto:owner-chemistry+mark==cresset-bmd.com-*-ccl.net] On Behalf Of Peter D Jarowski p.d.jarowski^^^surrey.ac.uk Sent: 10 December 2010 14:49 To: Mark Mackey Subject: CCL: Freeware Molecular Mechanics Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] Hello, Anyone know of a freeware molecular mechanics package with a reasonable GUI that runs on Mac intel? All I need is to run some preliminary minimizations and/or conformational searches before submitting to the cluster for QM. I know about Tinker, but I do not see a GUI for that one. Best, Peterhttp://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 Fri Dec 10 16:32:00 2010 From: "Utpal Sarkar utpalchemiitkgp(-)gmail.com" To: CCL Subject: CCL:G: Help for cluster Message-Id: <-43330-101210124958-4346-HUq3QXMh9NW7QOz4W67wCQ[-]server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: multipart/alternative; boundary=0015174be09423dea6049711fb1b Date: Fri, 10 Dec 2010 23:19:50 +0530 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp#gmail.com] --0015174be09423dea6049711fb1b Content-Type: text/plain; charset=ISO-8859-1 Dear Sir, We will do DFT using Gaussian upto say 50 atoms maximum and will not do HF or post HF. But using VASP we will try to do beyond 100 atoms ( big transition atom clusters , say 100 or 200 atoms in it). Side by side we will also run DL_POLY. So for this which one is the best configation? regards utpal On Thu, Dec 9, 2010 at 3:34 PM, Herbert Fruchtl herbert.fruchtl],[ st-andrews.ac.uk wrote: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl-x-st-andrews.ac.uk] > Very general questions. The answers depend on your mix of applications, > budget and level of expertise. I'll try to address a few points. > > > Utpal Sarkar utpalchemiitkgp[-]gmail.com wrote: > >> Dear CCL users, >> We are planning to purchase a 16 node (or >> even 32 node depending upon the price needed) cluser in which we will run >> softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly give >> your valuable suggestion about: >> a) which type of specification is better ? >> > > That's where the type of applications comes in: > > If it's mainly Gaussian, and mainly DFT calculations, get fast processors. > DFT doesn't need much memory (2GB/core is plenty), and most people run only > the SMP parallel version, so you don't need a fast network. If it's post-HF > calculations (MP2, CCSD, ...) you're after, get more memory. And if it's > beyond MP2, get a different program :-). > > If you want big VASP calculations (and they quickly get big), you need a > fast network (Infiniband) and possibly more memory. In a small cluster like > yours, you may get away with Gigabit Ethernet, but talk to somebody who has > tried it first. > > For force-field MD, you get incredible performance for little money from > GPUs, but it's still a bit experimental. Make sure the program you use > supports your hardware. There's a project under way for DL_POLY, but I don't > know if it's already available. > > > b) How much does it cost (we can spent upto $10K to $11K) ? >> > > Clusters are modular. You buy as many nodes as you can afford. Don't forget > storage. > > > c) does the company/ provider (ie, HP, Dell, SGI ets) will install the >> cluster in the lab or we have to install ourself? >> >> > You get what you pay for. They all sell turnkey solutions (i.e. fully > configured and installed). Buying just hardware and slapping ROCKS (or > something similar) on it is cheaper, but may cost you months of configuring. > If you're lucky it works immediately, but I have seen other cases... > > Hope this helps, > > Herbert > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0015174be09423dea6049711fb1b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sir,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 We will do DFT using Gaussian upto s= ay 50 atoms maximum and will not do HF or post HF. But using VASP we will t= ry to do beyond 100 atoms ( big transition atom clusters , say 100 or 200 a= toms in it). Side by side we will also run DL_POLY.
So for this which one is the best configation?
regards
utpal


=A0
On Thu, Dec 9, 2010 at 3:34 PM, Herbert Fruchtl = herbert.fruchtl],[st-andrews.ac.uk = <owner-chem= istry[A]ccl.net> wrote:

Sent to CCL by: Herbert Fruc= htl [herbert.fruchtl-x-st-andrews.ac.uk]
Very general questions. The answers depend on your mix of applications, bud= get and level of expertise. I'll try to address a few points.=20


Utpal Sarkar utpalchemiitkgp[-]gmail.com wrote:
Dear CCL users,
=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 We are planning to purchase= a 16 node (or even 32 node depending upon the price needed) cluser in whic= h we will run softwares like Gaussian, VASP, DLPOLY . So may I request you = to kindly give your valuable suggestion about:
a) which type of specification is better ?

That&#= 39;s where the type of applications comes in:

If it's mainly Gau= ssian, and mainly DFT calculations, get fast processors. DFT doesn't ne= ed much memory (2GB/core is plenty), and most people run only the SMP paral= lel version, so you don't need a fast network. If it's post-HF calc= ulations (MP2, CCSD, ...) you're after, get more memory. And if it'= s beyond MP2, get a different program :-).

If you want big VASP calculations (and they quickly get big), you need = a fast network (Infiniband) and possibly more memory. In a small cluster li= ke yours, you may get away with Gigabit Ethernet, but talk to somebody who = has tried it first.

For force-field MD, you get incredible performance for little money fro= m GPUs, but it's still a bit experimental. Make sure the program you us= e supports your hardware. There's a project under way for DL_POLY, but = I don't know if it's already available.=20


b) How much does it cost (we can= spent upto $10K to $11K) ?

Clusters are modular.= You buy as many nodes as you can afford. Don't forget storage.=20


c) does the company/ provider (i= e, HP, Dell, SGI ets) will install the cluster in the lab or we have to ins= tall ourself?
=A0
You get what you pay for. They all sell turnkey s= olutions (i.e. fully configured and installed). Buying just hardware and sl= apping ROCKS (or something similar) on it is cheaper, but may cost you mont= hs of configuring. If you're lucky it works immediately, but I have see= n other cases...

Hope this helps,

=A0Herbert
--
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 SC0= 13532=20




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--0015174be09423dea6049711fb1b-- From owner-chemistry@ccl.net Fri Dec 10 17:07:00 2010 From: "Victor Rosas Garcia rosas.victor::gmail.com" To: CCL Subject: CCL: Freeware Molecular Mechanics Message-Id: <-43331-101210154635-494-ATFRtM6U9SIKoNCZnEShYQ:server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 10 Dec 2010 14:46:00 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor^^^gmail.com] Take a look at Avogadro, there is a Mac version: http://avogadro.openmolecules.net/wiki/Get_Avogadro Nice GUI and has several force fields to choose from. Hope it helps. Victor 2010/12/10 Peter D Jarowski p.d.jarowski^^^surrey.ac.uk : > > Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] > Hello, > > Anyone know of a freeware molecular mechanics package with a reasonable GUI that runs on Mac > intel? All I need is to run some preliminary minimizations and/or conformational searches before > submitting to the cluster for QM. I know about Tinker, but I do not see a GUI for that one. > > Best, > > Peter From owner-chemistry@ccl.net Fri Dec 10 17:42:00 2010 From: "Reichert, David reichertd]|[mir.wustl.edu" To: CCL Subject: CCL: Mm with metals Message-Id: <-43332-101210170047-31167-GVIAUuinoCohbJ/+hSItHA- -server.ccl.net> X-Original-From: "Reichert, David" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_208330218E165F45AB6307B787F5EA476450992C11RADVMSRVEXV2r_" Date: Fri, 10 Dec 2010 16:00:31 -0600 MIME-Version: 1.0 Sent to CCL by: "Reichert, David" [reichertd]^[mir.wustl.edu] --_000_208330218E165F45AB6307B787F5EA476450992C11RADVMSRVEXV2r_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 VGhlIHByb2dyYW0gUEMtTW9kZWwgYnkgU2VyZW5hIFNvZnR3YXJlIGFuZCB0aGUgTU1YIGZvcmNl IGZpZWxkIGFjdHVhbGx5IGRvZXMgYSBwcmV0dHkgZ29vZCBqb2Igd2l0aCBtZXRhbCBjb21wbGV4 ZXMgYW5kIGhhcyBzb21lIHByZXR0eSBkZWNlbnQgb3B0aW9ucyBmb3IgY29uZm9ybWF0aW9uYWwg 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bmcgb2YNCiBhbnkgYWN0aW9uIGluIHJlbGlhbmNlIG9uIHRoZSBjb250ZW50cyBvZiB0aGlzIGlu Zm9ybWF0aW9uIGlzIHN0cmljdGx5IHByb2hpYml0ZWQuIElmIHlvdSBoYXZlIHJlY2VpdmVkIHRo aXMgZW1haWwgaW4gZXJyb3IsIHBsZWFzZSBpbW1lZGlhdGVseSBub3RpZnkgdGhlIHNlbmRlciB2 aWEgdGVsZXBob25lIG9yIHJldHVybiBtYWlsLjxicj4NCjwvZm9udD4NCjwvYm9keT4NCjwvaHRt bD4NCg== --_000_208330218E165F45AB6307B787F5EA476450992C11RADVMSRVEXV2r_-- From owner-chemistry@ccl.net Fri Dec 10 18:16:00 2010 From: "J Bredenbeck jbreden[#]gmx.de" To: CCL Subject: CCL:G: Relaxed surface scan with frequencies at each point Message-Id: <-43333-101210163731-21258-KFqFRi/OvzRpJUdgUsMRBw:_:server.ccl.net> X-Original-From: "J Bredenbeck" Date: Fri, 10 Dec 2010 16:37:22 -0500 Sent to CCL by: "J Bredenbeck" [jbreden!=!gmx.de] Dear CCL Users, I would like to do a relaxed surface scan in Gaussian03 with a normal mode calculation at each point after optimization. I would be great if somebody could tell me how this type of calculation can be set up. Regards, Jens From owner-chemistry@ccl.net Fri Dec 10 18:52:01 2010 From: "Gijs Schaftenaar schaft^-^cmbi.ru.nl" To: CCL Subject: CCL: Freeware Molecular Mechanics: Message-Id: <-43334-101210111002-5813-yRp7TfZzFByC4eBm8ZEMIA_+_server.ccl.net> X-Original-From: Gijs Schaftenaar Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 10 Dec 2010 17:09:50 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Gijs Schaftenaar [schaft * cmbi.ru.nl] There is molden which uses the amber/gaff force field: http://www.cmbi.ru.nl/molden Best Regards, Gijs Schaftenaar +----------------------------------------------------------------+ Gijs Schaftenaar, Dr. | Computational Drug Discovery, CMBI Email: | Radboud University of Nijmegen G.Schaftenaar=ncmls.ru.nl | Medical Centre / NCMLS, route 260 Tel. : +31 24 3619674 | Geert-Grooteplein 28 Fax : +31 24 3619395 | 6525 GA Nijmegen, The Netherlands +----------------------------------------------------------------+ On Fri, 10 Dec 2010, Peter D Jarowski p.d.jarowski^^^surrey.ac.uk wrote: > Date: Fri, 10 Dec 2010 09:49:28 -0500 > From: Peter D Jarowski p.d.jarowski^^^surrey.ac.uk > Reply-To: CCL Subscribers > To: "Schaftenaar, Gijs " > Subject: CCL: Freeware Molecular Mechanics > > > Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] > Hello, > > Anyone know of a freeware molecular mechanics package with a reasonable GUI that runs on Mac > intel? All I need is to run some preliminary minimizations and/or conformational searches before > submitting to the cluster for QM. I know about Tinker, but I do not see a GUI for that one. > > Best, > > Peter> > From owner-chemistry@ccl.net Fri Dec 10 22:32:01 2010 From: "=?ISO-8859-1?Q?Carlos_Javier_N=FA=F1ez?= carlosjavierna{=}gmail.com" To: CCL Subject: CCL: Freeware Molecular Mechanics Message-Id: <-43335-101210223106-9600-9ah6FTAGxNhUASNuchiZYQ()server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Carlos_Javier_N=FA=F1ez?= Content-Type: multipart/alternative; boundary=20cf3054a457870df504971a191c Date: Fri, 10 Dec 2010 21:31:00 -0600 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Carlos_Javier_N=FA=F1ez?= [carlosjavierna!A!gmail.com] --20cf3054a457870df504971a191c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, ArgusLab, http://www.arguslab.com/ Force fields: UFF and Amber (old) Semi-empirical calculations: PM3 and others. Two o three protocols of minimization. Number of minimization steps =3D variable. Only for Windows however. Carlos Javier El 10 de diciembre de 2010 08:49, Peter D Jarowski p.d.jarowski^^^ surrey.ac.uk escribi=F3: > > Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] > Hello, > > Anyone know of a freeware molecular mechanics package with a reasonable G= UI > that runs on Mac > intel? All I need is to run some preliminary minimizations and/or > conformational searches before > submitting to the cluster for QM. I know about Tinker, but I do not see a > GUI for that one. > > Best, > > Peter > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --20cf3054a457870df504971a191c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

ArgusLab,

http://www= .arguslab.com/


Force fields: UFF and Amber (old)
Semi-emp= irical calculations: PM3 and others.
Two o three protocols of minimizati= on.
Number of minimization steps =3D variable.
Only for Windows however.
=

Carlos Javier






El 10 de diciembre de 2010 08:49, Peter D Jarowski p.d.jarowski^^^surrey.ac.uk <owner-chemistry(_)ccl.net> escr= ibi=F3:

Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk]
Hello,

Anyone know of a freeware molecular mechanics package with a reasonable GUI= that runs on Mac
intel? All I need is to run some preliminary minimizations and/or conformat= ional searches before
submitting to the cluster for QM. I know about Tinker, but I do not see a G= UI for that one.

Best,

Peter



-=3D This is automatically added to each message by the mailing script =3D-=
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--20cf3054a457870df504971a191c-- From owner-chemistry@ccl.net Fri Dec 10 23:21:00 2010 From: "Kalju Kahn kalju^^chem.ucsb.edu" To: CCL Subject: CCL: Freeware Molecular Mechanics Message-Id: <-43336-101210215736-8959-qW3gB2xiEjHPIMjQ8YLRRg**server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 10 Dec 2010 18:57:06 -0800 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju,,chem.ucsb.edu] Peter, The workflow that I have used for preliminary conf analysis is: 1) Sketch structures in JME molecular editor via http://cactus.nci.nih.gov/services/translate/ 2) Import 3D structures into MOLDEN as MOL files and assign a suitable, TINKER-compatible force field 3) Optimize in MOLDEN, this generates a suitable TINKER .key file 4) Perform conformational analysis with TINKER (e.g. scan) 5) Analyze conformers with MOLDEN (has multi-molecule option) This worked on Macs few years ago (you need to set the environmental variable TNK_ROOT). The main challenge here is that the TINKER force fields that MOLDEN supports (i.e. MM3, Charmm, Amber, AmoebaPR) are limited in what kind of molecules they can handle. Doing simple structures with MM3 works well, but sooner or later you will run into missing dihedrals. More versatile force fields, such as OPLS or MMFF are not in MOLDEN, I am afraid. But since MOLDEN 4.8 we do have ambmd; I suppose you can do MD conformational sampling with Amber/GAFF force field. You can get more technical details from http://www.chem.ucsb.edu/~kalju/chem126/public/molecules_getting.html Hope this helps, Kalju > > Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk] > Hello, > > Anyone know of a freeware molecular mechanics package with a reasonable > GUI that runs on Mac > intel? All I need is to run some preliminary minimizations and/or > conformational searches before > submitting to the cluster for QM. I know about Tinker, but I do not see a > GUI for that one. > > Best, > > Peter> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106