From owner-chemistry@ccl.net Wed Nov 19 08:58:01 2008
From: "Thomsa Kuhlman kuhlman,+,nano.ku.dk" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Constrained optimization using Gaussian
Message-Id: <-38118-081118083110-8211-5tBYLYcZd0BnUHkvkyUIfg^server.ccl.net>
X-Original-From: "Thomsa  Kuhlman" <kuhlman]_[nano.ku.dk>
Date: Tue, 18 Nov 2008 08:31:06 -0500


Sent to CCL by: "Thomsa  Kuhlman" [kuhlman++nano.ku.dk]
Hi,

I'm am trying to do a constrained optimization on a part of a crystal structure using Gaussian. Basically it is part of an ab-plane of the crystal. I want to optimize part of this structure in the ab-plane which coincides with the xy-plane of my input coordinates and I do not want it to be able to move in the z-direction. Is there anyway to freeze the z-component using cartesian coordinates or is there anyway to achieve this constrained optimization in a plane?

Best regards,

Thomas


From owner-chemistry@ccl.net Wed Nov 19 10:59:01 2008
From: "Neha S Gandhi n.gandhiau[#]gmail.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian error
Message-Id: <-38119-081119091550-10876-36J60Oh/S1tPiepZrCIv0Q * server.ccl.net>
X-Original-From: "Neha S Gandhi" <n.gandhiau|-|gmail.com>
Date: Wed, 19 Nov 2008 09:15:46 -0500


Sent to CCL by: "Neha S Gandhi" [n.gandhiau,,gmail.com]
Hi All,

I am running Gaussian job as below:

%chk=penta.chk
%Mem=2GB
%NProc=4

#P hf/6-31G* Opt=(VTight,CalcFC) Freq SCF(Conver=8) Test nosymm

The walltime exceeds and I need to restart the job. How do I restart. When I restart (based on previous mailing list) I get the same errors. 

 dumping /fiocom/, unit = 2 NFiles =     8 SizExt =         0 WInBlk =      2048
                   defal = F LstWrd =     5763072 FType=2 FMxFil=10000

 Number           0        508        522        536        538        634        670        998
 Base       5762012      50048      50178    3858992    4810502      52936      40960      50078
 End        5763072      50078      52936    4810502    5762012    3858992      50048      50178
 End1       5763072      50078      52936    4810502    5762012    3858992      50048      50178
 Wr Pntr    5762012      50048      50178    3858992    4810502      52936      40960      50078
 Rd Pntr    5762012      50048      50178    3858992    4810502      52936      40960      50078
 Length        1060         30       2758     951510     951510    3806056       9088        100


 dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk =      2048
                   defal = T LstWrd =       65536 FType=2 FMxFil=10000

 Number           0
 Base         40960
 End          65536
 End1         65536
 Wr Pntr      40960
 Rd Pntr      40960
 Length       24576
 Error termination in NtrErr:
 NtrErr Called from FileIO.


 I tried following keywords with no luck.
%chk=penta.chk
%Mem=2GB
%NProc=4
#p hf/6-31g(d) opt=(calcfc,vtight,restart) scf(Conver=8) freq density=(current,checkpoint)nosymm geom=check test

Regards


From owner-chemistry@ccl.net Wed Nov 19 14:29:01 2008
From: "Nir London nir a rosettadesigngroup.com" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: The Macromolecular Modeling Blog
Message-Id: <-38120-081119121429-7941-7/BvtmUMduWwQW4IAfxbQg~!~server.ccl.net>
X-Original-From: "Nir  London" <nir(~)rosettadesigngroup.com>
Date: Wed, 19 Nov 2008 12:14:25 -0500


Sent to CCL by: "Nir  London" [nir],[rosettadesigngroup.com]
Hi all, and a special hi to the structural biology fans :) 

We've started a new blog on all that is related to Macromolecular Modeling 
http://rosettadesigngroup.com/blog/ 

We opened this blog in order to provide the modeling and computational structural biology 
community with a helpful resource. Keep updated with what's new in the modeling world, read 
executive summaries of the latest literature and stay in touch with pears. 

please check it out and tell me what you think... 
If any of you is interested in writing for the blog I'd be very happy if you contact me. 

Cheers, 
Nir London.
Rosetta Design Group
http://rosettadesigngroup.com


From owner-chemistry@ccl.net Wed Nov 19 15:04:01 2008
From: "=?ISO-8859-1?Q?=22MQO=2E_Carlos_Javier_N=FA=F1ez_Aguero=22?= carlosjavierna*gmail.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: HOMO y LUMO
Message-Id: <-38121-081119132754-15978-MB2qhHBMN7i+opuXdNrUiQ ~~ server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?=22MQO=2E_Carlos_Javier_N=FA=F1ez_Aguero=22?=
 <carlosjavierna]-[gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Wed, 19 Nov 2008 12:27:43 -0600
MIME-Version: 1.0


Sent to CCL by: =?ISO-8859-1?Q?=22MQO=2E_Carlos_Javier_N=FA=F1ez_Aguero=22?=
 [carlosjavierna!^!gmail.com]
Hi all,

the representation of the orbital molecular HOMO normally is in two 
colors: eg., red and blue, ok?
What means the colors? Red = negative density? Blue = positive density?

excuse for the question and for my english
Thanks in advance to all,
Regards,
Carlos Javier