From owner-chemistry@ccl.net Tue Aug 16 08:24:01 2011 From: "Emmeline Yeo emma.yeo2704_._gmail.com" To: CCL Subject: CCL:G: MD with DREIDING FF: system becomes unstable on inclusion of charges Message-Id: <-45261-110816042043-14968-yMqKILkVlE6HL8yvVutMMA]=[server.ccl.net> X-Original-From: "Emmeline Yeo" Date: Tue, 16 Aug 2011 04:20:40 -0400 Sent to CCL by: "Emmeline Yeo" [emma.yeo2704|-|gmail.com] Hi everyone, I'm new to force field molecular dynamics and will appreciate any advice that you can give on problem that I have. I was trying to simulate an amorphous polyacetylene polymer cell using the DREIDING force field with the program dl_poly. The system is stable and runs well if I set the atomic charges for all my atoms to zero. However, once I include the atomic charges (calculated using Gaussian program - and I checked, the values are reasonable and similar to another published paper), the system just becomes out of control: the total energy and the temperature of the system becomes very high. I don't think the problem lies with a bad initial configuration for the polymer as the same thing happens even if I just have 2 polymer chains in my periodic cell. An advice that I've been given is to ignore atomic charges except in the cases of simulating polyelectrolytes... Any other suggestions given is deeply appreciated! From owner-chemistry@ccl.net Tue Aug 16 09:04:00 2011 From: "Fatma Aksakal fatmaaksakal_-_gyte.edu.tr" To: CCL Subject: CCL: MD simulation package Message-Id: <-45262-110816085708-893-RG4R9l9ct8ALjU4UEF3lQg ~~ server.ccl.net> X-Original-From: "Fatma Aksakal" Date: Tue, 16 Aug 2011 08:57:05 -0400 Sent to CCL by: "Fatma Aksakal" [fatmaaksakal:+:gyte.edu.tr] Dear all, We are looking for a fast and reliable molecular dynamic simulation package (must be run on Windows platform). Could you suggest that kind of MD program? Thanks and regards. Fatma Fatma Aksakal fatmaaksakal#,#gyte.edu.tr Gebze Institute of Technology Chemistry Department Kocaeli/TURKEY From owner-chemistry@ccl.net Tue Aug 16 10:12:01 2011 From: "Sergio Manzetti sergio.manzetti()gmail.com" To: CCL Subject: CCL:G: Generating electrostatic potentials online Message-Id: <-45263-110816101004-28202-JGbuXZfLuxqnP2lT2Y96hQ{:}server.ccl.net> X-Original-From: Sergio Manzetti Content-Type: multipart/alternative; boundary=bcaec54859d24ddf5004aa9fef65 Date: Tue, 16 Aug 2011 16:09:58 +0200 MIME-Version: 1.0 Sent to CCL by: Sergio Manzetti [sergio.manzetti[-]gmail.com] --bcaec54859d24ddf5004aa9fef65 Content-Type: text/plain; charset=ISO-8859-1 Dear all, does anyone know of a program that generates EPS of molecules derived from Gaussian files online? Generating ESP takes awfully long time. Best regards S --bcaec54859d24ddf5004aa9fef65 Content-Type: text/html; charset=ISO-8859-1 Dear all, does anyone know of a program that generates EPS of molecules derived from Gaussian files online?

Generating ESP takes awfully long time.

Best regards

S
--bcaec54859d24ddf5004aa9fef65-- From owner-chemistry@ccl.net Tue Aug 16 12:09:00 2011 From: "Ciaran Murray ciaran.a.murray/a\nuim.ie" To: CCL Subject: CCL: Accelerated Molecular Dynamics Message-Id: <-45264-110816120710-15483-B0lBIVMRKZJkBFfJ6d+T+Q[]server.ccl.net> X-Original-From: "Ciaran Murray" Date: Tue, 16 Aug 2011 12:07:03 -0400 Sent to CCL by: "Ciaran Murray" [ciaran.a.murray{}nuim.ie] Hello CCLers, I'm interested in performing some accelerated molecular dynamics calculations in particular Art Voters parallel replica dynamics (see "Parallel replica method for dynamics of infrequent events" A. F. Voter, Phys. Rev. B 57, 13985 (1998)). Does anyone have any experience with these methods? If so, what code would you recommend? Thanks in advance, Ciarn Murray ciaran.a.murray==nuim.ie From owner-chemistry@ccl.net Tue Aug 16 12:44:00 2011 From: "Daniel Glossman-Mitnik dglossman]-[gmail.com" To: CCL Subject: CCL: Molecular modeling of ZnO/PP composite Message-Id: <-45265-110816124231-19188-zM6G3tHqQFwxLOSbGBwWmA(a)server.ccl.net> X-Original-From: Daniel Glossman-Mitnik Content-Type: multipart/alternative; boundary=bcaec52c5e59eaf58304aaa20a99 Date: Tue, 16 Aug 2011 10:40:51 -0600 MIME-Version: 1.0 Sent to CCL by: Daniel Glossman-Mitnik [dglossman|*|gmail.com] --bcaec52c5e59eaf58304aaa20a99 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear netters: I have been asked to try to simulate the optical properties of ZnO nanoparticles of varying size in a matrix of polypropilene (PP). I would like to know if you can give me hints about the appropiate methods and/or software to accomplish this task, and also about any reference to previous work in the subject. Thanks in advance. Best regards, Daniel ***************************************************************************= ************************************ Dr. Daniel Glossman-Mitnik Centro de Investigaci=C3=B3n en Materiales Avanzados, SC Departamento de Simulaci=C3=B3n Computacional y Modelado Molecular Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih 31109, Mexico Phone: +52 614 4391151 Secretary/FAX: +52 614 4391130 Lab: +52 614 4394805 E-mail: daniel.glossman.(a).cimav.edu.mx dglossman.(a).gmail.com WWW: http://www.cimav.edu.mx/cv/daniel.glossman http://blogs.cimav.edu.mx/daniel.glossman ***************************************************************************= ************************************ --bcaec52c5e59eaf58304aaa20a99 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear netters:

I have been asked to try to simulate the o= ptical properties of ZnO nanoparticles of varying size
in a matri= x of polypropilene (PP). I would like to know if you can give me hints abou= t the
appropiate methods and/or software to accomplish this task, and also a= bout any reference to
previous work in the subject.
Thanks in advance. Best regards,

Danie= l

*******************************************************= ********************************************************
Dr. Daniel Glos= sman-Mitnik
Centro de Investigaci=C3=B3n en Materiales Avanzados, SC
= Departamento de Simulaci=C3=B3n Computacional y Modelado Molecular
Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih 31109, Mex= ico
Phone: +52 614 4391151=C2=A0=C2=A0 Secretary/FAX: +52 614 4391130=C2= =A0 =C2=A0 Lab: +52 614 4394805
E-mail:=C2=A0 daniel.glossman.(a).cimav.edu.mx=C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 dglossman.(a).gmail.com
WWW:=C2=A0 http://ww= w.cimav.edu.mx/cv/daniel.glossman
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 http:/= /blogs.cimav.edu.mx/daniel.glossman
***************************************************************************= ************************************
--bcaec52c5e59eaf58304aaa20a99-- From owner-chemistry@ccl.net Tue Aug 16 13:19:01 2011 From: "pascal boulet pascal.boulet ~ univ-provence.fr" To: CCL Subject: CCL:G: MD with DREIDING FF: system becomes unstable on inclusion of charges Message-Id: <-45266-110816111741-808-2EDJULzJLg2FBYOH1oJFpA ~ server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 16 Aug 2011 17:17:22 +0200 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet]-[univ-provence.fr] Hello, When you say: "I checked, the values are reasonable and similar to another published paper " do you mean that the charges are reasonable or that the combination of the charges with the Dreiding FF are reasonable? The reason I ask the question is that probably you are "messing up" your FF by using these charges. They are probably not compatible with each other. Usually, FF parameters are fitted in conjunction with some specific charges in order to get an overall satisfactory force field. If you then change the charges the FF is no longer self-consistent. I think that Amber has been designed to work with ab initio charges. Perhaps you can adapt Amber parameters to your needs using your charges. Another option is to get the adequate charges for the Dreiding FF, if there are. You can get rid of the charges only if you have non polar chains in your polymer. otherwise, you will not describe properly e.g., hydrogen bonds (either intra or inter-molecular). If I were you, I would change the Dreiding FF for, e.g., cff91 or cff94, if compatible with DL_Poly. But, you first have to check if the corresponding energy terms are implemented in the program. [A]ARTICLE{Rappe1991, author = {Anthony K. Rappe and William A. Goddard}, title = {Charge equilibration for molecular dynamics simulations}, journal = {The Journal of Physical Chemistry}, year = {1991}, volume = {95}, pages = {3358--3363}, number = {8}, month = apr, abstract = {approach for predicting charge distributions in molecules for use in molecular dynamics simulations. Experimental atomic ionization potential, elctron affinities, atomic radii. Atomic chemical potential. shielded electrostatic interactions. Charge equilibration {QEq.} {CFF91} force field.}, doi = {10.1021/j100161a070}, keywords = {{CFF91}}, url = {http://dx.doi.org/10.1021/j100161a070} } Hope this help, Pascal Le 16/08/2011 10:20, Emmeline Yeo emma.yeo2704_._gmail.com a écrit : > Sent to CCL by: "Emmeline Yeo" [emma.yeo2704|-|gmail.com] > Hi everyone, > > I'm new to force field molecular dynamics and will appreciate any advice that > > you can give on problem that I have. > > > I was trying to simulate an amorphous polyacetylene polymer cell using the > > DREIDING force field with the program dl_poly. The system is stable and runs > > well if I set the atomic charges for all my atoms to zero. However, once I > > include the atomic charges (calculated using Gaussian program - and I > > checked, the values are reasonable and similar to another published paper), > > the system just becomes out of control: the total energy and the temperature > > of the system becomes very high. > > > I don't think the problem lies with a bad initial configuration for the > > polymer as the same thing happens even if I just have 2 polymer chains in my > > periodic cell. > > > An advice that I've been given is to ignore atomic charges except in the > > cases of simulating polyelectrolytes... > > > Any other suggestions given is deeply appreciated!> > > -- !!!!WARNING: my phone number has CHANGED!!!! Dr. pascal Boulet, computational chemist University of Aix-Marseille I Laboratoire Chimie Provence, UMR 6264 Group of Theoretical Chemistry Avenue Normandie-Niemen 13397 Marseille Cedex 20 France ********** Tel. (+33) (0)413.55.18.10 Fax. (+33) (0)491.55.18.50 ********** http://www.lc-provence.fr https://sites.google.com/a/univ-provence.fr/pb-comput-chem %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-chemistry@ccl.net Tue Aug 16 14:19:01 2011 From: "Masoud Nahali m_nahali[a]alum.sharif.edu" To: CCL Subject: CCL: lattice vector visualization by Chemcraft Message-Id: <-45267-110816124250-19354-wUBjmEtOKA1rA80pk+MxPA|a|server.ccl.net> X-Original-From: "Masoud Nahali" Date: Tue, 16 Aug 2011 12:42:46 -0400 Sent to CCL by: "Masoud Nahali" [m_nahali:_:alum.sharif.edu] Dear CCL Users Chemcraft can show the structure of my input file which includes 3 lattice vectors: C 0.00000000000000 0.00000000000000 13.22808268264000 C 0.00000000000000 2.68681136815000 13.22808268264000 ... ... TV 32.5759 0.0000 0.0000 TV -16.2879 28.2115 0.0000 TV 0.0000 0.0000 26.4562 but I could not find any option to visualize the vectors by Chemcraft, is there any option to do it ? I appreciate your help in advance. Best Wishes Masoud