From owner-chemistry@ccl.net Mon Sep 30 06:52:00 2013 From: "Adrian Stevens adrian.stevens*accelrys.com" To: CCL Subject: CCL: Announcing the release of Discovery Studio 4.0 Message-Id: <-49210-130930064937-11528-MFxjwMaRh9khpMkFV4usLw=server.ccl.net> X-Original-From: "Adrian Stevens" Date: Mon, 30 Sep 2013 06:49:36 -0400 Sent to CCL by: "Adrian Stevens" [adrian.stevens###accelrys.com] Accelrys is very pleased to announce the release of the latest version of Discovery Studio 4.0, our most complete and integrated solution for both biologics and small molecules-based research. Version 4.0 includes many new features and enhancements including: * Simulations sciences - Faster robust support for ns-scale MD simulations - Improved simulations workflow - Faster & robust Explicit solvation builder - Enhanced Molecular Dynamics analysis tools * Biologics research - New! Disulfide bond predictor - New! Multiple simultaneous mutations - Updated: Antibody database (Includes support to add your own antibody structures) - Updated: Antibody modeling workflows * Small-molecules drug research - New! Non-bond interaction monitors (including the most extensive set of favourable, unfavourable and unsatisfied interactions) - Updated In-situ FBDD lead optimization - Updated In-situ FBDD core-hopping tools - Updated Find Activity Cliffs using MMPs * Partner Science - CHARMm c37b2 (fully integrated charmm36 support) - NAMD v9.2 (New! NAMD is now included with Discovery Studio!) - MODELER 9v12 - DMol3 version 6.1 SP2 - VAMP version 10.0 - Updated support for CCDC's GOLD * Core/Platform - Significantly improved client memory management - Supports the latest Accelrys Enterprise Platform release (v9.1) Learn how to accelerate molecular simulations for your drug discovery research, with Discovery Studio 4.0! Register now for our live webinar series at http://accelrys.com/webinars/discovery-studio From owner-chemistry@ccl.net Mon Sep 30 07:27:00 2013 From: "thomas.bogaerts:ugent.be" To: CCL Subject: CCL:G: g09 frequency calculation error Message-Id: <-49211-130930041347-16028-EfSnuIES4i4+8Elo/U4gZg-#-server.ccl.net> X-Original-From: Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Mon, 30 Sep 2013 10:14:15 +0200 MIME-Version: 1.0 Sent to CCL by: [thomas.bogaerts..ugent.be] Dear Kursad, g09 uses two different algorithms to do a frequency calculation (solving the CPHF equations) The standard one uses a lot of RAM memory but is very fast. However when the number of CPHF equations exceeds 5000 by default gaussian uses another algorithm, this tries to save RAM memory by storing intermediate results on a hard disk. This takes very long making the calculations practically inactive. In order to solve this add an extra option: CPHF(MaxInv=10000). This puts the maximum number of CPHF equations for the basic algorithm to 10000. Make sure you have enough memory available when doing this. kind regards -----Original Message----- > From: kursad oguz patriscanary.:.gmail.com Sent: Sunday, September 29, 2013 4:06 AM To: Bogaerts, Thomas Subject: CCL:G: g09 frequency calculation error Sent to CCL by: "kursad oguz" [patriscanary- -gmail.com] Dear All, I am doing frequency calculation of some transition metal complex with gaussian 09 on linux based computer sistem. my all try ended with the same output. There is no error line end of output file. Please help me. Thanks in advance... my output is following. %nprocshared=16 Will use up to 16 processors via shared memory. %mem=8GB %chk=nibar.chk ------------------------------------------------------- # opt freq ub3lyp/genecp iop(5/10=-1) geom=connectivity ................... ................... ............... ................. End of G2Drv Frequency-dependent properties file 722 does not exist. IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111111 Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. There are 240 degrees of freedom in the 1st order CPHF. IDoFFX=5. 240 vectors produced by pass 0 Test12= 3.47D-13 1.00D-09 XBig12= 1.00D+03 6.30D+00. AX will form 36 AO Fock derivatives at one time. 240 vectors produced by pass 1 Test12= 3.47D-13 1.00D-09 XBig12= 4.46D+02 1.94D+00. 239 vectors produced by pass 2 Test12= 3.47D-13 1.00D-09 XBig12= 4.56D+00 1.58D-01. 237 vectors produced by pass 3 Test12= 3.47D-13 1.00D-09 XBig12= 2.34D- 02 1.32D-02. ................ ................... .................. ...................... ..................... 20 vectors produced by pass112 Test12= 3.47D-13 1.00D-09 XBig12= 1.66D- 14 2.54D-09. 20 vectors produced by pass113 Test12= 3.47D-13 1.00D-09 XBig12= 2.44D- 14 2.72D-09. 20 vectors produced by pass114 Test12= 3.47D-13 1.00D-09 XBig12= 4.54D- 14 4.87D-09. 20 vectors produced by pass115 Test12= 3.47D-13 1.00D-09 XBig12= 2.16D- 14 2.91D-09. 20 vectors produced by pass116 Test12= 3.47D-13 1.00D-09 XBig12= 2.34D- 14 2.92D-09. 20 vectors produced by pass117 Test12= 3.47D-13 1.00D-09 XBig12= 1.76D- 14 2.50D-09. 20 vectors produced by pass118 Test12= 3.47D-13 1.00D-09 XBig12= 1.93D- 14 2.65D-09. 20 vectors produced by pass119 Test12= 3.47D-13 1.00D-09 XBig12= 1.11D- 14 2.13D-09. 20 vectors produced by pass120 Test12= 3.47D-13 1.00D-09 XBig12= 3.34D- 14 3.87D-09. 19 vectors produced by pass121 Test12= 3.47D-13 1.00D-09 XBig12= 1.04D- 14 2.18D-09. 6 vectors produced by pass122 Test12= 3.47D-13 1.00D-09 XBig12= 4.62D- 15 1.17D-09. Applied DIIS recursively to reduced A of dimension 6486.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 Mon Sep 30 12:21:00 2013 From: "Partha Sengupta anapspsmo-$-gmail.com" To: CCL Subject: CCL: data below the no of imaginary frequency Message-Id: <-49212-130929144901-15660-Yjxfoes5uBH5mbqp05xMxg~~server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=047d7b15a779df3b5f04e78a2b1d Date: Mon, 30 Sep 2013 00:18:54 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo++gmail.com] --047d7b15a779df3b5f04e78a2b1d Content-Type: text/plain; charset=ISO-8859-1 Hello, All CCL user I am in query for a question. There is a lot of data after the no of imaginary frequency. as for example given below. What are these numbers? Waiting for reply Partha Sarathi Sengupta . NImag=1||0.87194168,0.03973045,0.64341951,0.37602276,-0.01 260824,0.41239695,-0.06250317,0.06427093,-0.05345900,0.57358802,0.0213 3547,-0.03660313,0.01609967,-0.12220700,0.95141832,-0.04949240,0.04047 935,-0.00953025,0.23429484,-0.13017701,0.31918798,-0.30843842,0.044054 42,-0.15109610,0.00258145,0.00028158,-0.00080338,0.31901925,0.04106014 ,-0.07435731,0.02525235,-0.00223104,-0.00735956,-0.00040112,-0.0439279 6,0.07549406,-0.15028717,0.02717171,-0.13210777,-0.00062570,0.00115654 ,0.00359341,0.16480395,-0.02810712,0.12625839,-0.00004034,0.00518729,- 0.00350309,-0.00013140,-0.00177362,-0.00261743,-0.00030873,-0.00071359 ,-0.00022576,0.54842834,0.00641785,-0.00334228,0.00321778,-0.02661088, -0.00522971,-0.01602228,0.00057823,0.00135019,0.00019260,-0.08051345,0 .64687612,-0.00355124,0.00472570,0.00272673,-0.00121559,-0.00019685,0. 00291987,-0.00063147,-0.00058936,0.00041904,0.06865189,0.01419455,0.57 334103,-0.00109087,0.00075529,-0.00030863,0.00115880,0.00038221,0.0011 8793,-0.00029889,-0.00039296,0.00003977,-0.12702028,0.08012729,-0.0965 4255,0.14616336,-0.00113695,0.00051281,-0.00019052,0.00006617,0.000718 48,0.00034948,-0.00022309,-0.00022865,0.00005127,0.08206266,-0.1517323 2,0.10524336,-0.08459517,0.16181705,-0.00033394,0.00031376,0.00013423, 0.00089668,-0.00003772,0.00108657,-0.00007266,-0.00015467,-0.00002372, -0.09515618,0.10403416,-0.17998012,0.10307679,-0.11816109,0.19653361,0 .00053068,-0.00163527,0.00032879,-0.00188047,0.00085355,-0.00188881,-0 .00004496,0.00010801,0.00004775,-0.09384254,0.08596263,0.04548539,-0.0 0692128,0.01479793,0.00920115,0.10604703,-0.00052137,-0.00120062,0.000 16693,-0.00115485,0.00080474,-0.00192432,-0.00000052,0.00003664,-0.000 08843,0.08467229,-0.24839748,-0.11117087,0.00657900,-0.01639113,-0.009 86303,-0.08579160,0.27159938,-0.00017758,-0.00120505,0.00018001,-0.000 47697,0.00051416,-0.00049804,-0.00000628,0.00007827,0.00003026,0.04429 235,-0.10669781,-0.11897601,-0.00918402,0.02207772,0.01420610,-0.05386 103,0.11907983,0.13059135,0.00036052,-0.00140715,-0.00035177,0.0006146 1,0.00245255,0.00091145,0.00013393,0.00011049,-0.00007109,-0.10357151, -0.00163433,0.04317216,0.00863493,0.00444082,-0.01265426,-0.01288879,- 0.00713730,0.01453084,0.51960649,-0.00030034,-0.00098831,-0.00009492,- 0.00154435,0.00096899,0.00006379,0.00000933,0.00001817,0.00002729,0.00 616332,-0.08848254,0.01535041,-0.01894679,-0.00741530,0.01991243,0.018 90122,0.00879749,-0.02186245,-0.08890436,0.66970396,0.00001307,-0.0009 3639,-0.00030256,-0.00081215,-0.00046491,-0.00075749,-0.00002696,-0.00 006059,-0.00015334,0.02160714,0.00971686,-0.13653913,0.02247778,0.0094 1456,-0.02399610,0.01699484,0.00825371,-0.01934643,0.00997200,0.101149 86,0.55367383,-0.00000408,0.00015051,0.00018607,0.00000212,-0.00052926 ,-0.00032841,-0.00001562,-0.00000841,0.00000989,-0.01034078,0.01742370 ,0.01282086,0.00113676,-0.00046560,-0.00055728,-0.00215487,-0.00207796 ,0.00292447,-0.10725818,0.09727289,0.05895985,0.11996473,0.00009066,0. 00019376,0.00005770,0.00025958,-0.00012428,-0.00009326,-0.00000252,-0. 00000898,0.00001093,-0.00712541,0.01228075,0.00745708,0.00056138,0.000 42033,-0.00074541,-0.00229692,-0.00039187,0.00250770,0.09143540,-0.239 61314,-0.11960866,-0.09562252,0.26405480,-0.00017319,-0.00011225,-0.00 015808,0.00000771,0.00030136,0.00025023,-0.00000070,0.00000180,-0.0000 0158,0.01355556,-0.02031823,-0.01330655,-0.00119635,-0.00026816,0.0006 6749,0.00277000,0.00231950,-0.00285273,0.05789757,-0.12467860,-0.13949 268,-0.06073444,0.12981708,0.15183800,-0.00241653,-0.00366378,-0.00116 613,0.00016837,0.00109722,0.00009822,-0.00015892,-0.00005695,-0.000136 87,0.02109821,-0.01736395,0.01944399,-0.00592881,-0.00210692,0.0062065 3,0.00016140,-0.00031015,0.00163526,-0.12224127,0.02923142,-0.01828769 ,-0.00706340,0.00792232,-0.01103228,0.40012671,-0.00096104,-0.00060422 ,-0.00036248,-0.00093821,-0.00143622,-0.00088626,0.00007269,0.00015152 ,0.00006837,-0.00249857,-0.01283405,0.01777286,-0.00009676,0.00026276, -0.00126723,0.00201492,0.00185551,-0.00529269,0.04481640,-0.12800032,0 ...... -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --047d7b15a779df3b5f04e78a2b1d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello, All CCL user I am in query for a question= . There is a lot of data after the no of imaginary frequency. as for exampl= e given below. What are these numbers?
Waiting for reply
Partha Sarathi Sengupta
=A0.
NImag=3D1||0.87194168,0.03973= 045,0.64341951,0.37602276,-0.01
=A0260824,0.41239695,-0.06250317,0.06427= 093,-0.05345900,0.57358802,0.0213
=A03547,-0.03660313,0.01609967,-0.1222= 0700,0.95141832,-0.04949240,0.04047
=A0935,-0.00953025,0.23429484,-0.13017701,0.31918798,-0.30843842,0.044054=A042,-0.15109610,0.00258145,0.00028158,-0.00080338,0.31901925,0.04106014=
=A0,-0.07435731,0.02525235,-0.00223104,-0.00735956,-0.00040112,-0.04392= 79
=A06,0.07549406,-0.15028717,0.02717171,-0.13210777,-0.00062570,0.00115654=A0,0.00359341,0.16480395,-0.02810712,0.12625839,-0.00004034,0.00518729,-=
=A00.00350309,-0.00013140,-0.00177362,-0.00261743,-0.00030873,-0.000713= 59
=A0,-0.00022576,0.54842834,0.00641785,-0.00334228,0.00321778,-0.02661088,=A0-0.00522971,-0.01602228,0.00057823,0.00135019,0.00019260,-0.08051345,0=
=A0.64687612,-0.00355124,0.00472570,0.00272673,-0.00121559,-0.00019685,= 0.
=A000291987,-0.00063147,-0.00058936,0.00041904,0.06865189,0.01419455,0.57=A0334103,-0.00109087,0.00075529,-0.00030863,0.00115880,0.00038221,0.0011=
=A08793,-0.00029889,-0.00039296,0.00003977,-0.12702028,0.08012729,-0.09= 65
=A04255,0.14616336,-0.00113695,0.00051281,-0.00019052,0.00006617,0.000718=A048,0.00034948,-0.00022309,-0.00022865,0.00005127,0.08206266,-0.1517323=
=A02,0.10524336,-0.08459517,0.16181705,-0.00033394,0.00031376,0.0001342= 3,
=A00.00089668,-0.00003772,0.00108657,-0.00007266,-0.00015467,-0.00002372,=A0-0.09515618,0.10403416,-0.17998012,0.10307679,-0.11816109,0.19653361,0=
=A0.00053068,-0.00163527,0.00032879,-0.00188047,0.00085355,-0.00188881,= -0
=A0.00004496,0.00010801,0.00004775,-0.09384254,0.08596263,0.04548539,-0.0=A00692128,0.01479793,0.00920115,0.10604703,-0.00052137,-0.00120062,0.000=
=A016693,-0.00115485,0.00080474,-0.00192432,-0.00000052,0.00003664,-0.0= 00
=A008843,0.08467229,-0.24839748,-0.11117087,0.00657900,-0.01639113,-0.009=A086303,-0.08579160,0.27159938,-0.00017758,-0.00120505,0.00018001,-0.000=
=A047697,0.00051416,-0.00049804,-0.00000628,0.00007827,0.00003026,0.044= 29
=A0235,-0.10669781,-0.11897601,-0.00918402,0.02207772,0.01420610,-0.05386=A0103,0.11907983,0.13059135,0.00036052,-0.00140715,-0.00035177,0.0006146=
=A01,0.00245255,0.00091145,0.00013393,0.00011049,-0.00007109,-0.1035715= 1,
=A0-0.00163433,0.04317216,0.00863493,0.00444082,-0.01265426,-0.01288879,-=A00.00713730,0.01453084,0.51960649,-0.00030034,-0.00098831,-0.00009492,-=
=A00.00154435,0.00096899,0.00006379,0.00000933,0.00001817,0.00002729,0.= 00
=A0616332,-0.08848254,0.01535041,-0.01894679,-0.00741530,0.01991243,0.018=A090122,0.00879749,-0.02186245,-0.08890436,0.66970396,0.00001307,-0.0009=
=A03639,-0.00030256,-0.00081215,-0.00046491,-0.00075749,-0.00002696,-0.= 00
=A0006059,-0.00015334,0.02160714,0.00971686,-0.13653913,0.02247778,0.0094=A01456,-0.02399610,0.01699484,0.00825371,-0.01934643,0.00997200,0.101149=
=A086,0.55367383,-0.00000408,0.00015051,0.00018607,0.00000212,-0.000529= 26
=A0,-0.00032841,-0.00001562,-0.00000841,0.00000989,-0.01034078,0.01742370=A0,0.01282086,0.00113676,-0.00046560,-0.00055728,-0.00215487,-0.00207796=
=A0,0.00292447,-0.10725818,0.09727289,0.05895985,0.11996473,0.00009066,= 0.
=A000019376,0.00005770,0.00025958,-0.00012428,-0.00009326,-0.00000252,-0.=A000000898,0.00001093,-0.00712541,0.01228075,0.00745708,0.00056138,0.000=
=A042033,-0.00074541,-0.00229692,-0.00039187,0.00250770,0.09143540,-0.2= 39
=A061314,-0.11960866,-0.09562252,0.26405480,-0.00017319,-0.00011225,-0.00=A0015808,0.00000771,0.00030136,0.00025023,-0.00000070,0.00000180,-0.0000=
=A00158,0.01355556,-0.02031823,-0.01330655,-0.00119635,-0.00026816,0.00= 06
=A06749,0.00277000,0.00231950,-0.00285273,0.05789757,-0.12467860,-0.13949=A0268,-0.06073444,0.12981708,0.15183800,-0.00241653,-0.00366378,-0.00116=
=A0613,0.00016837,0.00109722,0.00009822,-0.00015892,-0.00005695,-0.0001= 36
=A087,0.02109821,-0.01736395,0.01944399,-0.00592881,-0.00210692,0.0062065=A03,0.00016140,-0.00031015,0.00163526,-0.12224127,0.02923142,-0.01828769=
=A0,-0.00706340,0.00792232,-0.01103228,0.40012671,-0.00096104,-0.000604= 22
=A0,-0.00036248,-0.00093821,-0.00143622,-0.00088626,0.00007269,0.00015152=A0,0.00006837,-0.00249857,-0.01283405,0.01777286,-0.00009676,0.00026276,=
=A0-0.00126723,0.00201492,0.00185551,-0.00529269,0.04481640,-0.12800032= ,0
......

--
Dr. Partha Sarathi Sengupta
Asso= ciate Professor
Vivekananda Mahavidyalaya, Burdwan
--047d7b15a779df3b5f04e78a2b1d--