From owner-chemistry@ccl.net Sat May 28 09:16:01 2011 From: "bertho bertho||univ-montp2.fr" To: CCL Subject: CCL: way to convert .cif file to a complete lattice Message-Id: <-44779-110527150141-16152-FD5eaQUjUmALNAryVa0QjQ*|*server.ccl.net> X-Original-From: bertho Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 27 May 2011 21:01:20 +0200 MIME-Version: 1.0 Sent to CCL by: bertho [bertho:univ-montp2.fr] You can use molden (windows and linux). It reads .cif files and you can save as xyz and .mol etc ... Best regards Dorothée Berthomieu On Fri, 27 May 2011 15:47:50 +0200, "Jerome Kieffer Jerome.Kieffer---terre-adelie.org" wrote: > Sent to CCL by: Jerome Kieffer [Jerome.Kieffer---terre-adelie.org] > On Fri, 27 May 2011 05:49:55 -0400 > "Bhaskarjyoti Borah bhaskargreen%%gmail.com" > wrote: > >> >> Sent to CCL by: "Bhaskarjyoti Borah" [bhaskargreen**gmail.com] >> Dear all, >> >> I am having a situation here. I have a .cif file of a zeolite framework >> obtained from zeolite database. Now I want to obtain the super lattice( >> say one unit cell of the zeolite lattice in real coordinates) of the >> zeolite. Does anybody know any program which can do this for me? Or if >> anybody has some script to do this, could you kindly share the same with >> me. Any suggestions will be highly appreciated. Thanks in advance. >> > > Use Mercury (from the CCDC) which has this nice "bug" of saving all atoms > displayed: > -open the cif > -display full cell > -save as xyz From owner-chemistry@ccl.net Sat May 28 09:51:00 2011 From: "Amrita Kumari amrita.g13 : gmail.com" To: CCL Subject: CCL: how to model system for MD simulation Message-Id: <-44780-110528093428-624-4b0GUEBGGFzCXxjrSJN4hQ..server.ccl.net> X-Original-From: Amrita Kumari Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 28 May 2011 19:04:22 +0530 MIME-Version: 1.0 Sent to CCL by: Amrita Kumari [amrita.g13||gmail.com] Hi, I want to know that how can I model the system for MD simulation means which software I can use to build the system for MD simulation. our system is CNT inside water environment and we are interested in looking at the dynamics of water molecule inside CNT. We want to use TINKER for getting the dynamics and it uses .xyz file as input to do the dynamics calculation. So how can I get .xyz file for our system? Thanks, Amrita Kumari Research Scholar IISER Mohali Chandigarh (INDIA) From owner-chemistry@ccl.net Sat May 28 17:12:00 2011 From: "Guilherme Luis Cordeiro guilhermecord%%gmail.com" To: CCL Subject: CCL: Doubt on Optmization Output Message-Id: <-44781-110528171045-30923-S20erQOBbBT8bfgjsMDaWA{=}server.ccl.net> X-Original-From: "Guilherme Luis Cordeiro" Date: Sat, 28 May 2011 17:10:43 -0400 Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord~!~gmail.com] Dears members, I started performing an optmization on a flavonoid system containing around 30 atoms surrounded by 3 ethanol molecules. First calculation began with AM1 method, then I used this as a starting point for a new minimization with B3LYP/3-21G model chemistry. The job finished like this: Item Value Threshold Converged? Maximum Force 0.000004 0.000450 YES RMS Force 0.000001 0.000300 YES Maximum Displacement 0.041333 0.001800 NO RMS Displacement 0.006043 0.001200 NO Predicted change in Energy=-2.049104D-07 Optimization completed on the basis of negligible forces. -- Stationary point found. The geometry obtained, then, is being used on another minimization with B3LYP/6-31G. Should restart it all over? What does mean the "negligible forces" term? Thanks in advance. Guilherme Cordeiro. From owner-chemistry@ccl.net Sat May 28 20:07:01 2011 From: "Brian Salter-Duke b_duke=-=bigpond.net.au" To: CCL Subject: CCL: Doubt on Optmization Output Message-Id: <-44782-110528194419-16311-1ClQb8qIXk3bzTxxvhHrzQ:_:server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sun, 29 May 2011 09:41:55 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke#,#bigpond.net.au] On Sat, May 28, 2011 at 05:10:43PM -0400, Guilherme Luis Cordeiro guilhermecord%%gmail.com wrote: > > Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord~!~gmail.com] > Dears members, > > I started performing an optmization on a flavonoid system containing around 30 atoms surrounded by 3 ethanol molecules. First calculation began with AM1 method, then I used this as a starting point for a new minimization with B3LYP/3-21G model chemistry. The job finished like this: > > Item Value Threshold Converged? > Maximum Force 0.000004 0.000450 YES > RMS Force 0.000001 0.000300 YES > Maximum Displacement 0.041333 0.001800 NO > RMS Displacement 0.006043 0.001200 NO > Predicted change in Energy=-2.049104D-07 > Optimization completed on the basis of negligible forces. > -- Stationary point found. > The geometry obtained, then, is being used on another minimization > with B3LYP/6-31G. Should restart it all over? What does mean the > "negligible forces" term? What it says. Look at the Maximum Force and RMS Force values. They are very small. The surface is very flat so the forces are small and the predicted displacements for the next step are large and never going to get small, so it stops. You can try restarting with a different basis set. It might work. Brian. > Thanks in advance. > > Guilherme Cordeiro.> -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: b_duke_-_bigpond.net.au Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm From owner-chemistry@ccl.net Sat May 28 23:51:01 2011 From: "Ahmed E. Ismail aei^alum.mit.edu" To: CCL Subject: CCL: how to model system for MD simulation Message-Id: <-44783-110528144147-25794-2q6OkDNDGgVgGsaitoS4gw(~)server.ccl.net> X-Original-From: "Ahmed E. Ismail" Content-Type: multipart/alternative; boundary=20cf3043459c70000f04a45a67b7 Date: Sat, 28 May 2011 20:41:36 +0200 MIME-Version: 1.0 Sent to CCL by: "Ahmed E. Ismail" [aei]![alum.mit.edu] --20cf3043459c70000f04a45a67b7 Content-Type: text/plain; charset=ISO-8859-1 Hello Amrita: Unfortunately, there's no magic solution to putting together a configuration file. You may able to use some online tools (such as PRODRG) or software like Materials Studio to set up the simulation, but it still requires active involvement on your part to get it done. The only exception to this is if someone has chosen to share their xyz (or other) coordinate file as public domain (for instance, in the "supporting information" section of an online paper. Even then, though, you will still need to make sure that the file is appropriate for your use. --AEI ========================= Ahmed E. Ismail aei^_^alum.mit.edu aei^_^aya.yale.edu --20cf3043459c70000f04a45a67b7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hello Amrita:

Unfortunately, t= here's no magic solution to putting together a configuration file. You = may able to use some online tools (such as PRODRG) or software like Materia= ls Studio to set up the simulation, but it still requires active involvemen= t on your part to get it done.

The only exception to this is if someone has chosen to = share their xyz (or other) coordinate file as public domain (for instance, = in the "supporting information" section of an online paper. Even = then, though, you will still need to make sure that the file is appropriate= for your use.

--AEI=A0
=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
Ahmed E. Ismail
aei^_^alum.mit.edu
aei^_^aya.yale.= edu

--20cf3043459c70000f04a45a67b7--