From owner-chemistry@ccl.net Sat Apr 1 03:50:00 2006 From: "Lee Sang Uck sulee/a\imr.edu" To: CCL Subject: CCL: G03 Electric Field Message-Id: <-31374-060401034536-32487-HoDEEnBG54Dl6BhfKvDBdQ~~server.ccl.net> X-Original-From: "Lee Sang Uck" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0000_01C655AE.70B3F470" Date: Sat, 1 Apr 2006 17:05:12 +0900 MIME-Version: 1.0 Sent to CCL by: "Lee Sang Uck" [sulee(-)imr.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0000_01C655AE.70B3F470 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear all, Now I'm calculating some system under electric field. In my doing, I'd like to know the difference between a small molecule and a large molecule under same applied electric field. If I used the option of "Field=x+20", it could be converted to about "1V/angstrom ". So, when I used 1 angstrom length molecule (A) and 10 angstrom length molecule (B), I'd like to know the difference between them. In the case of B, is it right that I considered the applied field as 10 V, because the molecular size is 10 angstroms? Thank you for your time. Regards, Sang Uck Lee ==================================================== Sang Uck Lee Laboratory of Materials Design by Computer Simulation Institute for Materials Research Tohoku University, Japan sulee-x-imr.edu http://user.chol.com/~deugilg/ ==================================================== ------=_NextPart_000_0000_01C655AE.70B3F470 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear all,

 

Now I’m calculating some system under electric = field.

In my doing, I’d like to know the = difference between a small molecule and a large molecule under same applied = electric field.

If I used the option of “Field=3Dx+20”, it = could be converted to about “1V/angstrom = “.

So, when I used 1 angstrom length molecule (A) and 10 angstrom length molecule (B), I’d like to know the = difference between them.

In the case of B, is it right that I considered the = applied field as 10 V, because the molecular size is 10 = angstroms?

 

Thank you for your time.

Regards,

Sang Uck Lee

 

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

Sang Uck Lee

Laboratory of Materials = Design by Computer Simulation

Institute for Materials Research

Tohoku = University, Japan

sulee-x-imr.edu=

http://user.chol.com/~deugilg/

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

 

------=_NextPart_000_0000_01C655AE.70B3F470-- From owner-chemistry@ccl.net Sat Apr 1 04:24:01 2006 From: "Lee Sang Uck sulee(!)imr.edu" To: CCL Subject: CCL:G: G03 SCF converge Message-Id: <-31375-060401034530-32447-jKXyb/fcQsdm5DtgMxa8EA,server.ccl.net> X-Original-From: "Lee Sang Uck" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01C655AF.E2644E20" Date: Sat, 1 Apr 2006 17:15:33 +0900 MIME-Version: 1.0 Sent to CCL by: "Lee Sang Uck" [sulee * imr.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0004_01C655AF.E2644E20 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear All, I'd like to know the meaning of BMatC and BMatP of G03 output file. I guessed that they are related to DIIS process. However I could not understand exactly. When I achieved a SCF convergence, the values of them become small. ErrMax= 7.34D-02 EMaxC= 1.00D-01 BMatC= 1.09D+00 BMatP= 1.36D-12 Sometimes, even though I got a convergence of density matrix and energy as like following, RMSDP=1.48D-08 MaxDP=7.12D-07 DE=-3.99D-06 OVMax= 2.63D-06 the BMatC value is still large. So, I'd like to know how I can achieve a SCF convergence properly. Thank you for your time. Regards, Sang Uck Lee ==================================================== Sang Uck Lee Laboratory of Materials Design by Computer Simulation Institute for Materials Research Tohoku University, Japan sulee###imr.edu http://user.chol.com/~deugilg/ ==================================================== ------=_NextPart_000_0004_01C655AF.E2644E20 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear All,

 

I’d like to know the meaning of BMatC and BMatP of G03 output = file.

I guessed that they are related to DIIS process. = However I could not understand exactly.

When I achieved a SCF convergence, the values of them = become small.

 

 ErrMax=3D 7.34D-02 EMaxC=3D 1.00D-01 BMatC=3D 1.09D+00 = BMatP=3D 1.36D-12

 

Sometimes, even though I got a convergence of density = matrix and energy as like following,

 

RMSDP=3D1.48D-08 MaxDP=3D7.12D-07 DE=3D-3.99D-06 = OVMax=3D 2.63D-06

 

the BMatC value is still large.   So, = I’d like = to know how I can achieve a SCF convergence properly.

 

Thank you for your time.

 

Regards,

Sang Uck Lee

 

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

Sang Uck Lee

Laboratory of Materials = Design by Computer Simulation

Institute for Materials Research

Tohoku = University, Japan

sulee###imr.edu=

http://user.chol.com/~deugilg/

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

------=_NextPart_000_0004_01C655AF.E2644E20-- From owner-chemistry@ccl.net Sat Apr 1 11:11:00 2006 From: "Geoffrey Hutchison grh25##cornell.edu" To: CCL Subject: CCL: XYZ to PDB translation Message-Id: <-31376-060331183351-19218-37K8EDXne2BYxfhFMQsZfQ]_[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Fri, 31 Mar 2006 16:29:40 -0500 Mime-Version: 1.0 (Apple Message framework v746.3) Sent to CCL by: Geoffrey Hutchison [grh25{:}cornell.edu] Dear Mikhail, As I've posted several times on CCL, there are several e-mail lists for discussing Open Babel and support. There's also a form to report bugs at the main webpage: http://openbabel.sourceforge.net/ > 1. Is there any way to make OpenBabel work with big files without > any errors? Well, if you can e-mail me a test file, I'll certainly take a look. I work with fairly large files, although I don't think we've tested a 15-20MB file yet. Does this system involve biomolecules (and thus the translation to PDB)? Or do you not care about residue information? Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruņa Group http://abruna.chem.cornell.edu/ On Mar 31, 2006, at 2:16 PM, Mikhail Ladanov mladanov:mail.usf.edu wrote: > Sent to CCL by: "Mikhail Ladanov" [mladanov/./mail.usf.edu] > I work with MD simulations of system with very big number of atoms. > Im trying to translate my XYZ file into PDB using OpenBabel 2.0 > As soon as I have a file of size about 15-20 Mb, Babel results with > segmentation fault. > I have therefore 2 questions: > 1. Is there any way to make OpenBabel work with big files without > any errors? > 2. Is there any other utility I could translate XYZ to PDB with? From owner-chemistry@ccl.net Sat Apr 1 11:50:01 2006 From: "Senthil Kumar senthilkumar_natesan^-^bi.iiita.ac.in" To: CCL Subject: CCL: DOCK-flexibase ligands from ZINC Message-Id: <-31377-060401103838-698-ijjrHPyRfOjKxies8iwioQ:+:server.ccl.net> X-Original-From: "Senthil Kumar" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 1 Apr 2006 20:08:29 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Senthil Kumar" [senthilkumar_natesan * bi.iiita.ac.in] Dear All, I would be very thankful if anyone could explain me how to use DOCK-flexibase ligands from ZINC Thanks in advance. Senthil Kumar Natesan, M.Tech(IT), Final sem., specialization in Bioinformatics, Indian Institute of Information Technology, Allahabad, India 211012. cell: 09235717853 other mail ID: sen.natesan..gmail.com From owner-chemistry@ccl.net Sat Apr 1 12:25:00 2006 From: "Senthil Kumar Natesan senthilkumar_natesan(_)bi.iiita.ac.in" To: CCL Subject: CCL: DOCK-parallel processing-linux clusters Message-Id: <-31378-060401115456-27486-ZpspcMw8olfp8RyLNccoHQ:+:server.ccl.net> X-Original-From: "Senthil Kumar Natesan" Date: Sat, 1 Apr 2006 11:54:54 -0500 Sent to CCL by: "Senthil Kumar Natesan" [senthilkumar_natesan===bi.iiita.ac.in] Dear Colleagues, Pls suggest me in detail, 1. How to setup linux clusters for parallel processing (4 machines), i.e assigining master and slave nodes? 2. Should I install MPI and DOCK on all systems or? I would be very thankful if anyone could explain me all steps. sincerely, senthil kumar From owner-chemistry@ccl.net Sat Apr 1 13:00:01 2006 From: "Shireen Alfalah shireen.alfalah * yahoo.com" To: CCL Subject: CCL: software to convert name into structure Message-Id: <-31379-060401123939-19123-xceIf6IsKGpvsqaPhK/SDQ_+_server.ccl.net> X-Original-From: Shireen Alfalah Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1568940659-1143909564=:75530" Date: Sat, 1 Apr 2006 08:39:24 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Shireen Alfalah [shireen.alfalah ~ yahoo.com] --0-1568940659-1143909564=:75530 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL users, I am wondering if there is a free software that can convert the name of a compound into chemical structure. I am aware of the pubchem but it just gives the structure in image format. I am wondering if there is a free software that can convert the name into structure with a format that hyperchem (for example) or any other molecular building software can read. Thanks in advance. ************************************** Sherin Alfalah PhD Student Theoretical Chemist Chemistry Department AlQuds University ************************************** --------------------------------- New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-1568940659-1143909564=:75530 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCL users,
I am wondering if there is a free software that can convert the name of a compound into chemical structure. I am aware of the pubchem but it just gives the structure in image format. I am wondering if there is a free software that can convert the name into structure with a format that hyperchem (for example) or any other molecular building software can read.
 
Thanks in advance.
 
 
 


**************************************
Sherin Alfalah
PhD Student
Theoretical Chemist
Chemistry Department
AlQuds University
**************************************

New Yahoo! Messenger with Voice. Call regular phones from your PC and save big. --0-1568940659-1143909564=:75530-- From owner-chemistry@ccl.net Sat Apr 1 16:00:00 2006 From: "Praveen Depa praveen_depa]_[yahoo.com" To: CCL Subject: CCL: problem with LAMMPS Message-Id: <-31380-060401143010-4437-RhV1HDCWQaLw7vKHD6EGkw#%#server.ccl.net> X-Original-From: Praveen Depa Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 1 Apr 2006 10:30:03 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Praveen Depa [praveen_depa|*|yahoo.com] Hi all, I am trying to use LAMMPS, an open source parallel MD code, to simulate polymer chains (eg. polyethylene) using united atom force fields. I tried to use 'in.chain' and 'data.chain' provided in '/lammps/tools' with some modifications to start the simulation. But it keeps crashing on me and my guess is its due to the magnitude of the resulting forces. Those files in /tools are for FENE chains (320 chains with 100 beads per chain) and the units are reduced in 'lj' units. I dont have a good feel for the reduced units and hence cant figure out a way around the problem. Can any one who uses LAMPPS pls provide me with an example for the input files for polymers with united atom potentals in either real or reduced units. Also, does any know a method to generate the initial configuration for arbitrary number of chain lengths and number of chains. Thanx in advance -Praveen. -------------------- Praveen Depa PhD Student Penn State Univ PA, USA email: pdepa^^engr.psu.edu -------------------- __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sat Apr 1 21:53:00 2006 From: "Rajan Vatassery r-vatassery a northwestern.edu" To: CCL Subject: CCL: Summing Electron Density Message-Id: <-31381-060401215053-17097-FWHsQgjQQQredKzFaQQKUQ]=[server.ccl.net> X-Original-From: "Rajan Vatassery" Date: Sat, 1 Apr 2006 21:50:53 -0500 Sent to CCL by: "Rajan Vatassery" [r-vatassery()northwestern.edu] r-vatassery a northwestern.edu Dear CCLers, I am working on a problem involving high harmonic generation and I have the need for a very accurate assessment of the spatial electron distribution in the HOMO of N2 and the HOMO of O2. I have calculated the structures of both (trivially) using GAMESS-US and I plan on summing up the contributions of each basis function (from 6-31++G**) to each HOMO. I have read Dr Labanowski's document at http://www.ccl.net/cca/documents/basis-sets/basis.html but I still have a few small concerns that I may be doing something wrong. First, according to the GAMESS .log file, in the 6-31++G** basis set for O2, I have 19 basis functions per oxygen, where I only count 17 in the basis set coefficient numbers listed here (parentheses and numbers inside are my count): SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S) O 6 S 1 5484.6716600 0.001831074430(1) 6 S 2 825.2349460 0.013950172200(2) 6 S 3 188.0469580 0.068445078098(3) 6 S 4 52.9645000 0.232714335992(4) 6 S 5 16.8975704 0.470192897984(5) 6 S 6 5.7996353 0.358520852987(6) 7 L 7 15.5396162 -0.110777549525(7) 0.07087426(13) 7 L 8 3.5999336 -0.148026262701(8) 0.33975283(14) 7 L 9 1.0137618 1.130767015354(9) 0.72715857(15) 8 L 10 0.2700058 1.000000000000(10)1.00000000(16) 9 L** 11 0.0845000 1.000000000000(11)1.00000000(17) 10 D 12 0.8000000 1.000000000000(12) This is obviously a simple error on my part, but I'm sure someone else has made the same mistake. If you have, could you please let me know what is wrong, or point me to resources that have helped you? Secondly, and finally, I don't know what the last L function (the one with the double asterisk) is referring to. I can assume it's a diffuse function, but I can't find the coefficient in my .log file that would match it in my O2 molecule. I can see from Dr Labanowski's document that the 'S' in my .log file corresponds to the spherically symmetric function (any of 1-6 numbered above), and that the 'Y' corresponds to the spherically symmetric function (any of 13-16) times displacement along y, but I can't figure out which coefficient in my .log file goes with the last 'L' (11 or 17). Any help is greatly appreciated. Rajan Vatassery Graduate Student From owner-chemistry@ccl.net Sat Apr 1 23:31:00 2006 From: "Rajan Vatassery r-vatassery|,|northwestern.edu" To: CCL Subject: CCL: please disregard the second part of my last post Message-Id: <-31383-060401230137-26647-hqU1GQ/Hoz+7RZoplGdmDQ-#-server.ccl.net> X-Original-From: "Rajan Vatassery" Date: Sat, 1 Apr 2006 23:01:35 -0500 Sent to CCL by: "Rajan Vatassery" [r-vatassery _ northwestern.edu] Please ignore the second part of my last post. Sorry for the unnecessary emails.