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alick_cxjгæ (СÓÐÃûÆø)
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¸ß˹¸Õ¸Õ¿ªÊ¼Ñ§²»¾Ã£¬»ù±¾É϶¼²»Ôõô¶®£¬¹ÊÏò¸÷λÇë½Ì¡£ ÎÒÔÚ֮ǰ²»¿¼ÂÇÈܼÁЧӦʱÊÇ¿ÉÒÔÓÅ»¯³É¹¦µÄ£¬µ«¿¼ÂǺó¾ÍÒ»Ö±³ö´í£¬²»ÖªµÀÔõô»ØÊ£¬Çë¸÷λ°ïæ¿´¿´Ó¦¸ÃÔõô½â¾ö£¬Ð»Ð»ÁË ´íÎó£º Polarizable Continuum Model (PCM) ================================= Model : C-PCM. Atomic radii : UFF (Universal Force Field). Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=0.200 OFac=0.890). Default sphere list used, NSphG= 52. Tesserae with average area of 0.200 Ang**2. 1st derivatives : Analytical q*S(x)*q algorithm for C-PCM (CSMder). Cavity 1st derivative terms included. Solvent : Ethanol, Eps = 24.550000 Eps(inf)= 1.847000 RSolv = 2.180000 Ang. ------------------------------------------------------------------------------ BldSpC: Error generating genealogic tree for sphere 365 at level 15 Error termination via Lnk1e in /home/xjchen/g03/l301.exe at Mon Nov 7 18:59:31 2011. Job cpu time: 5 days 17 hours 29 minutes 31.5 seconds. File lengths (MBytes): RWF= 1318 Int= 0 D2E= 0 Chk= 38 Scr= 1 ÊäÈëÎļþ£º %chk=P1_cpcm.chk %mem=500MW %nproc=8 # opt freq pbe1pbe/6-31+g(d) scrf=(cpcm,solvent=ethanol,read) iop(1/8=5) P1_cpcm 0 1 ×ø±ê¡¡ Radii=UFF |
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alick_cxj
гæ (СÓÐÃûÆø)
- Ó¦Öú: 2 (Ó×¶ùÔ°)
- ½ð±Ò: 902
- Ìû×Ó: 52
- ÔÚÏß: 16.6Сʱ
- ³æºÅ: 1307761
- ×¢²á: 2011-05-27
- ÐÔ±ð: GG
- רҵ: ÀíÂۺͼÆË㻯ѧ
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¶î£¬»¹ÊÇûÈ˻ظ´°¡ ÎÒ°ÑGaussian¸øÎҵĻظ´Ìù³öÀ´£¬´ó¼Ò¿´¿´°É£¬¸ß˹¹«Ë¾»Ø¸´»¹Í¦¿ìµÄ£¬×òÌìÏÂÎçÎÊ£¬½ñÌìÔçÉϾÍÊÕµ½ÓʼþÁË¡£ Thank you for your inquiry. This is a geometrical problem regarding the generation of the solute cavity by the PCM models. Most of the difficulties with PCM in G03 were of this nature. The generation of the solute cavity in the G03 PCM implementation was made out of a series of interlocking spheres centered in the atoms of the molecule and determined by the chosen radii. In addition to this, the cavity generator included a number of additional spheres to smooth the surface, which are important around the edges where the atom-centered spheres interlock. The added spheres however can add too much complexity and problems associated with very small tesserae, which can make geometry optimizations difficult to converge. The most problematic cases for geometry optimizations in G03 are cage-like structures, weakly bound complexes consisting of several molecules, organometallic compounds whose ligands are close to each other, etc. The G03-style cavity tried to fill in some of the empty space with added spheres. Also, on some symmetric systems, the generation of the solute cavity may be problematic. Note that G09 features a new formalism for computing the reaction field that ensures continuity, smoothness and robustness, including continuous derivatives with respect to atomic positions and external perturbing fields. This formalism, initially proposed in 1999 by Karplus and York [York99], has been developed and generalized for whole the PCM family of solvation methods [Scalmani09]. This is achieved by expanding the apparent surface charge that builds up at the solute-solvent interface ("Polarization charges" in terms of spherical Gaussian functions located at each surface element in which the cavity surface is discretized. Discontinuities in the surface derivatives are removed by effectively smoothing the regions where the spheres intersect, which also eliminates the need for the problematic "added spheres" used in the default G03 solute cavities to smooth the cavity surfaces. For new studies, we recommend the use of PCM in the new G09 implementation in order to avoid this type of problems. If you still use G03, you may try to reduce the number of added spheres. The addition of spheres to smooth the surface cavity in PCM models is controlled by the "RMin" and "OFac" PCM options (additional PCM keywords to be included at the end of your input file). These parameters are the minimum radius for any added sphere and the maximum overlap between spheres, respectively. The default values for these parameters are "RMin=0.2" and "OFac=0.89", so, for instance, #p RMin=0.5 OFac=0.8 will increase the minimum size of the additional spheres (RMin > default), and reduce the number of these spheres (OFac < default) resulting in a smaller total number of added spheres than in the default case. By modifying the parameters this way with respect to the default values (that is by reducing the number of added spheres), the solute cavity will become a bit rougher but it will not change the overall shape of the cavity. The default OFac and RMin values ("RMin=0.2" and "OFac=0.89" are generally appropriate for most cases. The values shown above ("RMin=0.5" and "OFac=0.8" generally work well when problems with the cavity appear. Any intermediate values between the default values and the ones given here may also be acceptable. Keep in mind that the modification of the "OFac" and "RMin" parameters will make changes in the total energy that may be noticeable. Thus, the safest choice will be to use the same "OFac" and "RMin" values for the generation of the cavities in all the PCM calculations for this same study, so the cavities in each case are comparable, and so will be the energies. Sincerely, Fernando R. Clemente, Ph.D. Technical Support Gaussian, Inc. help@gaussian.com |
2Â¥2011-11-09 10:22:32
·¹·¹316
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3Â¥2011-11-09 13:17:43
xiongb123456
ͳæ (СÓÐÃûÆø)
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alick_cxj(½ð±Ò+1): ûÈ˻شð¾Í¸øÄãÁ衃 2011-11-10 09:33:36
zhou2009:±à¼ÄÚÈÝ 2011-11-14 08:47
zhou2009(½ð±Ò+3): 2011-11-14 08:49:23
alick_cxj(½ð±Ò+1): ûÈ˻شð¾Í¸øÄãÁ衃 2011-11-10 09:33:36
zhou2009:±à¼ÄÚÈÝ 2011-11-14 08:47
zhou2009(½ð±Ò+3): 2011-11-14 08:49:23
|
¸ß˹¹«Ë¾µÄ»Ø¸´ ÊÇÈÃÄ㠸IJÎÊýÂ£¿¡°RMin=0.5 OFac=0.8¡±²»ÒªÓÃĬÈÏÖµÁË ÄãÒª²»ÌýÌý¸ß˹µÄ ×Ô¼ºÐ´¸öRMin=0.5 OFac=0.8ÔÚºóÃæ ÊÔÊÔ°É ÎÒ×î½üËãÈܼÁЧӦÓõÄÊÇPCM ²»ÊÇCPCM ÎÒÒ²ÊÇÐÂÊÖ ÔÀ´²»»áµÄ»¹¿ÉÒÔÎʸß˹¹«Ë¾ ѧϰÁË [ Last edited by zhou2009 on 2011-11-14 at 08:47 ] |
4Â¥2011-11-09 16:43:28
·¹·¹316
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- Ó¦Öú: 0 (Ó×¶ùÔ°)
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- ³æºÅ: 956894
- ×¢²á: 2010-02-20
- רҵ: ¹âÆ×·ÖÎö
5Â¥2011-11-09 19:12:31
alick_cxj
гæ (СÓÐÃûÆø)
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6Â¥2011-11-09 22:43:22
alick_cxj
гæ (СÓÐÃûÆø)
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7Â¥2011-11-09 22:44:46
xiongb123456
ͳæ (СÓÐÃûÆø)
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- רҵ: µç»¯Ñ§
8Â¥2011-11-14 08:14:32
alick_cxj
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- ×¢²á: 2011-05-27
- ÐÔ±ð: GG
- רҵ: ÀíÂۺͼÆË㻯ѧ
9Â¥2011-11-14 10:21:19













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in terms of spherical Gaussian functions located at each surface element in which the cavity surface is discretized. Discontinuities in the surface derivatives are removed by effectively smoothing the regions where the spheres intersect, which also eliminates the need for the problematic "added spheres" used in the default G03 solute cavities to smooth the cavity surfaces.