From owner-chemistry@ccl.net Sun Nov 26 09:40:00 2006 From: "Alvyn Liang alvyn.liang|*|gmail.com" To: CCL Subject: CCL: Parallel programming (looking for help) Message-Id: <-33076-061126093923-22750-eXfyFkFbrDCD+FW6uDLh3g^_^server.ccl.net> X-Original-From: "Alvyn Liang" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 26 Nov 2006 14:39:14 +0000 MIME-Version: 1.0 Sent to CCL by: "Alvyn Liang" [alvyn.liang#gmail.com] Hi Is there anyone good in parallel programming. I need help on modifying my code. I have a C++ code which previously written for GNU gcc. Now I need it to work with a new machine that support MPI. Please mail me if you are interested in helping me. Thank you very much Alvyn From owner-chemistry@ccl.net Sun Nov 26 15:02:00 2006 From: "Adlane sayede adlane.sayede*_*gmail.com" To: CCL Subject: CCL:G: Incomplete coordinate system Message-Id: <-33077-061126115405-29903-kTTB3WWR72C6rcqjbzfyug:server.ccl.net> X-Original-From: "Adlane sayede" Content-Type: multipart/alternative; boundary="----=_Part_4228_23965381.1164556226271" Date: Sun, 26 Nov 2006 16:50:26 +0100 MIME-Version: 1.0 Sent to CCL by: "Adlane sayede" [adlane.sayede^_^gmail.com] ------=_Part_4228_23965381.1164556226271 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, everyone While I was doing the optimization with G03 in the pm3 level, I got the following error : GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Use GDIIS/GDPIS optimizer. SLEqS1 Cycle: 10201 Max:0.274569E-05 RMS:0.607538E-06 Conv:0.284595E-10 Incomplete coordinate system. Try restarting with Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) Incomplete coordinate system. Error termination via Lnk1e in /usr/oem/g03_D02/g03/l103.exe at Sat Nov 25 20:17:52 2006. Job cpu time: 0 days 9 hours 19 minutes 47.4 seconds. File lengths (MBytes): RWF= 201 Int= 0 D2E= 0 Chk= 110 Scr= 2 Can anyone tell me what's going on? Thanks a lot. A. Sayede ------=_Part_4228_23965381.1164556226271 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline 
Hi, everyone
 While I was doing the optimization with G03 in the pm3 level, I got the
 following error :

GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
 Berny optimization.

 Use GDIIS/GDPIS optimizer.
 SLEqS1 Cycle: 10201 Max:0.274569E-05 RMS:0.607538E-06 Conv:0.284595E-10
 Incomplete coordinate system.  Try restarting with
 Geom=Check Guess=Read Opt=(ReadFC,NewRedundant)
 Incomplete coordinate system.

 Error termination via Lnk1e in /usr/oem/g03_D02/g03/l103.exe at Sat Nov 25 20:17:52 2006.
 Job cpu time:  0 days  9 hours 19 minutes 47.4 seconds.
 File lengths (MBytes):  RWF=    201 Int=      0 D2E=      0 Chk=    110 Scr=      2



 Can anyone tell me what's going on?
 Thanks a lot.

A. Sayede
------=_Part_4228_23965381.1164556226271-- From owner-chemistry@ccl.net Sun Nov 26 17:13:00 2006 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas a chem.elte.hu" To: CCL Subject: CCL:G: Incomplete coordinate system Message-Id: <-33078-061126170807-30676-AM0UO36eQGtpRkR9CD3Aog##server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sun, 26 Nov 2006 23:08:16 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas ~~ chem.elte.hu] Hi Adlane, The error message indicates that the transformation of Cartesian forces to internals did not converge (for semiempiricals, the "large molecular" iterative transformations are used by default, Opt=Small changes that but may need more memory and much more CPU time, but no guarantee that it solves the original problem). This usually means that due to changes in the molecular geometry the initially built redundant internal coordinate system should be changed. Building up a new coordinate system usually helps in such situations (the error message gives this advice). If the error message came in the first optimization cycle or the adviced restart did not solve the problem than the internal coordinates should be examined and some manual modifications can help. If you think that the automatically generated coordinate system should be manually changed please add some trivial H-bonds or send me the structure directly and hopefully I can make the necessary changes. For testing the coordinate system you can use an MM optimization with the Opt=Large option. Best wishes, Ödön On Sun, 2006-11-26 at 15:28 -0500, Adlane sayede adlane.sayede*_*gmail.com wrote: > > Hi, everyone > While I was doing the optimization with G03 in the pm3 level, I got the > following error : > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > Berny optimization. > Use GDIIS/GDPIS optimizer. > SLEqS1 Cycle: 10201 Max:0.274569E-05 RMS:0.607538E-06 Conv:0.284595E-10 > Incomplete coordinate system. Try restarting with > Geom=Check Guess=Read Opt=(ReadFC,NewRedundant) > Incomplete coordinate system. > Error termination via Lnk1e in /usr/oem/g03_D02/g03/l103.exe at Sat > Nov 25 20:17:52 2006. > Job cpu time: 0 days 9 hours 19 minutes 47.4 seconds. > File lengths (MBytes): RWF= 201 Int= 0 D2E= 0 Chk= > 110 Scr= 2 > > > Can anyone tell me what's going on? > Thanks a lot. > > A. Sayede > -- Ödön Farkas Research associate professor Deparment of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Sun Nov 26 23:21:00 2006 From: "fuji fuji yamafuji6/a\yahoo.com" To: CCL Subject: CCL:G: Protonation and g03 Message-Id: <-33079-061126231928-23415-P/NpAAeHFDP/SmlBoxYutg,,server.ccl.net> X-Original-From: "fuji fuji" Date: Sun, 26 Nov 2006 23:19:28 -0500 Sent to CCL by: "fuji fuji" [yamafuji6]|[yahoo.com] dear all, My molecule have two protonation sites (say for example N2 and N5). But at pH=7 there is only one protonated form exists in addition with the unprotonated form (around 50:50). So, I would like to analyze the protonation site at pH=7. Is it possible to do it in g03? if so wat kind of calculations i can perform? Analytical frequency calculations with MP2/6-311+G(d) level gave me all real frequencies for N2 protonated form and two negative frequencies for N5 protonated form. Is this enough to proove that N2 protonation is favorable? (also, experimental results are in good agreement with this) Is it possible to include the pH effect in a g03 calculation? if so please give me the syntax/keyword. Looking forward for your reply. Thank you very much.