From owner-chemistry@ccl.net Tue Dec 9 07:40:01 2014 From: "FyD fyd * q4md-forcefieldtools.org" To: CCL Subject: CCL: Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 Message-Id: <-50807-141209033628-6071-oZK/3J9WR4n2ph98FALhQQ|,|server.ccl.net> X-Original-From: FyD Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 09 Dec 2014 09:36:18 +0100 MIME-Version: 1.0 Sent to CCL by: FyD [fyd**q4md-forcefieldtools.org] Dear All, I am pleased to announce the release of the R.E.D. Server Development/PyRED version November 2014 at q4md-forcefieldtools.org: http://q4md-forcefieldtools.org/REDServer-Development/ Among the new developed features this version handles the Amber non-additive force field model: - i. e. generation of polarizable force fields. The list of the new features developed in this version is available at: http://q4md-forcefieldtools.org/REDServer-Development/Bugs-NewFeatures.txt Documentation has been updated: http://q4md-forcefieldtools.org/REDServer-Development/Documentation/ New tutorials are available at: http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php The 'Re_Fit' mode, as well as the 'Complex' mode and the broken symmetry approach developed for bioinorganic complexes are described. Force field generation with lone-pairs and/or extra-points, using GAFF, OPLS and the Glycam 2004/2006 force fields, and generation of Amber polarizable force fields are also demonstrated. R.E.D. Server Development interfaces the RESP program version 2.4 or 3.1: http://q4md-forcefieldtools.org/REDServer-Development/resp/ This project is funded by the “Conseil Regional de Picardie” and the “European Regional Development Fund”. It results from a joined project between the Universite de Picardie - Jules Verne (Amiens, France) and the Sanford-Burnham Medical Research Institute (San Diego, USA) regards, Francois F.-Y. Dupradeau --- http://q4md-forcefieldtools.org/FyD/ From owner-chemistry@ccl.net Tue Dec 9 11:23:01 2014 From: "Oliver Stueker ostueker_._gmail.com" To: CCL Subject: CCL: Choosing appropriate OPLS parameters for Tetrolic Acid Message-Id: <-50808-141209083737-11492-EmlQljclorNDOsyaeQrt3A%x%server.ccl.net> X-Original-From: Oliver Stueker Content-Type: multipart/alternative; boundary=001a11c3c784160ca90509c8a574 Date: Tue, 9 Dec 2014 10:07:31 -0330 MIME-Version: 1.0 Sent to CCL by: Oliver Stueker [ostueker{:}gmail.com] --001a11c3c784160ca90509c8a574 Content-Type: text/plain; charset=UTF-8 Dear Conor, please be aware that simulating linear molecules can cause numerical problems, as the dihedreal (torsion) angles containing the C#C bond (19-19) are ill defined. E.g.: Try to measure the torsion angles "4-3-19-19" and "46-13-19-19" when the "3-19-19" and "13-19-19" angles are 180 degrees. You haven't specified the goal of your simulation, but in case you are planning to use bond-constraints, you might want to treat the alkyne C's as virtual sites, spaced appropriately along a C(carboxyl), C(methyl) "bond" (with a bond length of d(C-COOH)+d(C#C)+d(C-CH3) ). Of course you would need to fit appropriate dihedreal potentials for types: 46 13 3 4 46 13 3 5 > from semi-empirical or ab-initio calculations. Depending whether or not virual sites in lammps (I've never used lammps) can have a mass you might need to do more tricks to get a molecule with the correct mass and moment of inertia. This tutorial, written for creating a CO2 topology in Gromacs, covers these points. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html That said, you need to judge if a model with a rigid C-C#C-C unit is suitable for what you want to do. Good luck, Oliver On Sun, Dec 7, 2014 at 7:40 PM, conor douglas parks coparks2012=gmail.com < owner-chemistry]=[ccl.net> wrote: > > Sent to CCL by: "conor douglas parks" [coparks2012.]=[.gmail.com] > Hello, I am in the process of performing my first molecular dynamics > simulations for an actual research > project, and have some questions regarding the choice of the appropriate > force field parameters from > the OPLS parameter set. My molecule is Tetrolic acid, and has what I > believe are the following atom > types > > > atom# atom type atom symbol description > 209 3 C carboxylic acid > COOH > 210 4 O carboxylic acid > C=O > 211 5 OH carboxylic acid > -OH > 212 7 HO carboxylic acid > -COOH > 769 19 CZ alkyne RCCR > 80 13 CT Alkane CH3 > 85 46 HC alkane H-C > > Now from what I can tell, I believe the following angles need to be > specified for Tetrolic acid > > 4 3 5 > 3 5 7 > 4 3 19 > 13 19 19 > 19 19 3 > 19 13 46 > > I can not find any parameters for the angle bending for the 19-19-3 angle > in the OPLS parameter set > (http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm). Does anyone > have any suggestions of > how I could obtain a suitable parameter for this type of interaction? > > Similary for the torsion, I believe I need parameters for > > 4 3 5 7 > 7 5 3 19 > 4 3 19 19 > 46 13 19 19 > > However, I cannot find any parameters for the 46 13 19 19 group or the 4 3 > 19 19. Similarly, are there > any suggestions for what I can do here? Are there any issues with the atom > types I have selected for > tetrolic acid? The two triple bonded C have given me some concern. > --001a11c3c784160ca90509c8a574 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Conor,

please be aware that s= imulating linear molecules can cause numerical problems, as the dihedreal (= torsion) angles containing the C#C bond (19-19) are ill defined.
E.g.: Try to measure the torsion angles "4-3-19-19" and= "46-13-19-19" when the "3-19-19" and "13-19-19" angles are 180 degrees.


You haven't specified the goal of your simulation, but in case yo= u are planning to use bond-constraints, you might want to treat the alkyne = C's as virtual sites, spaced appropriately along a C(carboxyl), C(methy= l) "bond" (with a bond length of d(C-COOH)+d(C#C)+d(C-CH3) ).

Of course you would need to fit appropriate dihedreal pot= entials for types:
46 13 =C2=A03 4
46 13 =C2=A03 5<= br>
from semi-empirical or ab-initio calculations.

=
Depending whether or not virual sites in lammps (I've never us= ed lammps) can have a mass you might need to do more tricks to get a molecu= le with the correct mass and moment of inertia.

This t= utorial, written for creating a CO2 topology in Gromacs, covers these point= s.
http://www.bevanlab.biochem.vt.edu/Pa= ges/Personal/justin/gmx-tutorials/vsites/index.html

That said, you need to judge if a model with a rigid = C-C#C-C unit is suitable for what you want to do.

Good luck,
Oliver

On Sun, Dec 7, 2014 at 7:40 PM, co= nor douglas parks coparks2012=3Dgmail.com = <owner-chemistry]=[ccl.net> wrote:

Sent to CCL by: "conor douglas parks" [coparks2012.]=[.gmail.com]
Hello, I am in the process of performing my first molecular dynamics simula= tions for an actual research
project, and have some questions regarding the choice of the appropriate fo= rce field parameters from
the OPLS parameter set. My molecule is Tetrolic acid, and has what I believ= e are the following atom
types


atom#=C2=A0 =C2=A0 =C2=A0atom type=C2=A0 =C2=A0 =C2=A0 =C2=A0atom symbol=C2= =A0 =C2=A0 =C2=A0 description
209=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 C=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0carboxylic acid COOH
210=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 O=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0carboxylic acid C=3DO
211=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 5=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 OH=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0carboxylic acid -OH
212=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 7=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HO=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0carboxylic acid -COOH
769=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 19=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 CZ=C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0alkyne RCCR
80=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 13=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 CT=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Alkane CH3
85=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 46=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 HC=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0alkane H-C

Now from what I can tell, I believe the following angles need to be specifi= ed for Tetrolic acid

4=C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A0 5
3=C2=A0 =C2=A0 5=C2=A0 =C2=A0 =C2=A0 7
4=C2=A0 =C2=A0 3=C2=A0 =C2=A0 =C2=A019
13=C2=A0 =C2=A019=C2=A0 19
19=C2=A0 =C2=A019=C2=A0 =C2=A03
19=C2=A0 =C2=A013=C2=A0 =C2=A046

I can not find any parameters for the angle bending for the 19-19-3 angle i= n the OPLS parameter set
(http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm). Does anyone have any suggestions of
how I could obtain a suitable parameter for this type of interaction?

Similary for the torsion, I believe I need parameters for

4 3 5 7
7 5 3 19
4 3 19 19
46 13 19 19

However, I cannot find any parameters for the 46 13 19 19 group or the 4 3 = 19 19. Similarly, are there
any suggestions for what I can do here? Are there any issues with the atom = types I have selected for
tetrolic acid? The two triple bonded C have given me some concern.

--001a11c3c784160ca90509c8a574-- From owner-chemistry@ccl.net Tue Dec 9 13:15:01 2014 From: "Goedele Roos groos+*+vub.ac.be" To: CCL Subject: CCL: winterschool computational chemistry Message-Id: <-50809-141209131347-30411-I0n5Hm8VsIH6pEEkWXOe1A _ server.ccl.net> X-Original-From: Goedele Roos Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Tue, 09 Dec 2014 19:13:41 +0100 MIME-Version: 1.0 Sent to CCL by: Goedele Roos [groos*|*vub.ac.be] Dear CCL, It is a great tradition to share information among scientists. Since we strongly believe in this principle, we're organizing 'Winterschool' on Computational Chemistry from 3-10 Feb 2015. This 'Winterschool on Computational Chemistry' is a virtual congres with lectures from (young) scientists (PhD/post-doc). Rather than discussing cutting edge research, the aim is more educational and to provide theoretical background presented by our excellent speakers. Every day of the congres, you will be served 2 or 3 inspiring scientists. On 7 and 8 Feb, there will be a meet and greet session: no lectures will be released, but participants will be challenged to present their work and to exchange insights with their peers in our social corner. Registration is free, but required to access the lectures and the discussion fora. Please check our website http://winterschool.cc and our linked-in group https://www.linkedin.com/groups?home=&gid=8208925 for more information. Hoping to meet you all on Winterschool, Best wishes, the organizers, Ramasami Ponnadurai, Julianna Oláh and Goedele Roos _____________________________ Goedele Roos, PhD Department of General Chemistry http://we.vub.ac.be/~algc/ VIB, Department of Structural Biology, Vrije Universiteit Brussel | http://www.structuralbiology.be/ Brussels Center for Redox Biology | http://redox.vub.ac.be/ Vrije Universiteit Brussel, Building G, room 10G714 Pleinlaan 2, 1050 Brussels,Belgium phone: +32 2 6293312 fax: +32 2 6293317 E-mail: groos%a%vub.ac.be From owner-chemistry@ccl.net Tue Dec 9 15:01:01 2014 From: "Goedele Roos groos%%vub.ac.be" To: CCL Subject: CCL: small correction in previous mail about winterschool Message-Id: <-50810-141209145911-19140-BtDTh5VEM6DS1zO811ALQw(0)server.ccl.net> X-Original-From: Goedele Roos Date: Tue, 09 Dec 2014 20:59:03 +0100 Sent to CCL by: Goedele Roos [groos],[vub.ac.be] Dear ccl, in the previous mail this was stated: This 'Winterschool on Computational Chemistry' is a virtual congres with lectures from (young) scientists (PhD/post-doc). of course the 'from' needs to be changed in 'for scientists', because we have excellent professors as speakers Goedele _____________________________ Goedele Roos, PhD Department of General Chemistry http://we.vub.ac.be/~algc/ VIB, Department of Structural Biology, Vrije Universiteit Brussel | http://www.structuralbiology.be/ Brussels Center for Redox Biology | http://redox.vub.ac.be/ Vrije Universiteit Brussel, Building G, room 10G714 Pleinlaan 2, 1050 Brussels,Belgium phone: +32 2 6293312 fax: +32 2 6293317 E-mail: groos:vub.ac.be From owner-chemistry@ccl.net Tue Dec 9 16:32:00 2014 From: "Eric Schwegler schwegler1+/-llnl.gov" To: CCL Subject: CCL: 2015 Computational Chemistry and Materials Science Summer Institute Message-Id: <-50811-141209160236-15528-PBr6OyQ3Gu1C2h2YNXcCKA[-]server.ccl.net> X-Original-From: "Eric Schwegler" Date: Tue, 9 Dec 2014 16:02:35 -0500 Sent to CCL by: "Eric Schwegler" [schwegler1_._llnl.gov] We are pleased to announce the 2015 Computational Chemistry and Material Science (CCMS) Summer Institute, which will take place from June 8 - August 14, 2015 at Lawrence Livermore National Laboratory (LLNL). The goal of the Summer Institute is to provide graduate students with the opportunity to work directly with LLNL researchers on the development and application of cutting edge methods in computational materials science and chemistry and other related areas. The 2015 CCMS Summer Institute will have a special focus on "Mesoscale Materials and Chemistry" to reflect the ever increasing interest and enormous research opportunities in mesoscale phenomena, where classical, nanoscale and quantum science meet. Each student will spend ten weeks at LLNL as a guest of an LLNL host scientist working on a computational project in the host's area of expertise. In addition, leading researchers from universities and national labs will give a series of mini-courses for the students. These courses will cover state-of-the-art and emerging computational methods in materials science and chemistry. Travel funds and a generous stipend will be provided to the participants. In order to be considered, prospective participants will need to fill out an application form that can be found at the following website: www.llnl.gov/ccms/ The application deadline is February 9, 2015. We would greatly appreciate it if you could bring this announcement to the attention of graduate students that you feel would benefit from the experience of hands-on research in computational chemistry and materials science, working with leading researchers at a national laboratory. Additional details about the summer institute can be found on the website listed above. Eric Schwegler (schwegler1~!~llnl.gov) Felice Lightstone (felice~!~llnl.gov) From owner-chemistry@ccl.net Tue Dec 9 17:53:01 2014 From: "Juan Torras joan.torras~~upc.edu" To: CCL Subject: CCL:G: Software announcement: Release of PUPIL 3.0 Message-Id: <-50812-141209162747-22694-5tHrVfTFXE04V4vaWBcYyQ^server.ccl.net> X-Original-From: "Juan Torras" Date: Tue, 9 Dec 2014 16:27:46 -0500 Sent to CCL by: "Juan Torras" [joan.torras**upc.edu] We are pleased to announce the release of PUPIL 3.0. PUPIL (Program for User Package Interface and Linking), is a software environment that allows users and developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. * Graphic User Interface to build the main simulation input file. * Simulation Manager to lead the multi-scale simulation between different external programs. * Interface with Amber v10, 11, 12, and 14 * Interface with DeMon2k 4.2.4 * Interface with DL_CLASS_1.9 (DLPOLY) * Interface with NWChem v6.1.1 and v6.5 * Interface with Gaussian 03 and 09 * Interface with Siesta v3.2 (Start/Stop and CycleQM behaviors) * Interface with MNDO97 (Start/Stop QM role behaviors) * stubMD. Stub program for interface sample and testing playing a Molecular Dynamics Calculation Unit role. * stubQM. Stub program for interface sample and testing, playing a Cycle Quantum Mechanics Calculation Unit role. * stubDI. Stub program for interface sample and testing,playing an external Domain Identifier Calculation Unit role. New Features: * DL_CLASS program incorporates the electrostatic embedding scheme through the PUPIL interface. * PUPIL package has been updated to be compatible with Java 1.7 and 1.8. * A new interface with NWChem 6.3 and 6.5. * Some bottle-neck on the neighborhood rules has been fixed through the parallelization on the PUPIL core. * An initial alpha version using Long-range electrostatics on the QM region has been implemented * More accurate numerical checks are incorporated when the output files of tests cases are compared. For full details of PUPIL's features and capabilities, visit our web page: http://pupil.sourceforge.net/ The PUPIL Team.