From owner-chemistry@ccl.net Tue Feb 2 04:14:00 2010 From: "Silvio a Beccara s.abeccara . gmail.com" To: CCL Subject: CCL: Born radii for GROMOS96 force field Message-Id: <-41162-100202033337-5387-l3qT1mT3l0zAqT4B8+J9Pw ~~ server.ccl.net> X-Original-From: Silvio a Beccara Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 2 Feb 2010 08:57:07 +0100 MIME-Version: 1.0 Sent to CCL by: Silvio a Beccara [s.abeccara-,-gmail.com] Dear list friends, I am planning to use the OpenMM library to address protein folding problems. I would like to use the GROMOS96 force field, but I also need to employ the Generalized Born/Surface Area model to take into account solvent effects implicitly. In the Gromacs/OpenMM distribution a parameters file is supplied (params.agb), but it can only be used along with the Amber force field. Could anybody provide me with a valid parameter file for the GROMOS96 43a2 force field? Thanks in advance Silvio a Beccara University of Trento - Italy From owner-chemistry@ccl.net Tue Feb 2 05:00:02 2010 From: "Anton Lopis aslopis[-]gmail.com" To: CCL Subject: CCL: Computing Thermal Conductivity Message-Id: <-41163-100202044914-24866-oVhRLIXxehi691cisnc4vw^-^server.ccl.net> X-Original-From: Anton Lopis Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 2 Feb 2010 11:48:55 +0200 MIME-Version: 1.0 Sent to CCL by: Anton Lopis [aslopis^^gmail.com] Hi Pascal, Thanks for the reply and suggestion Pascal, appreciate it. Yes, DL_POLY2 (2.18) does of course calculate the forces for each atom and can write them in the trajectory (history) file. Unfortunately these do not appear to be the forces - or energies - required for thermal conductivity analysis. DL-POLY yields the forces on each atom due to all the other atoms (from the gradient of the potential). What I believe I require is forces F_ij, that is the forces on atom i due to only atom j. It is the Embedding function which causes the complications - since it depends on all the surrounding atoms (via the electron density contributions), not just atom j. Energy contributions are also complicated in this way. The same issues remain if one reformulates the current density j: j =3D d/dt (SUM E_i*r_i) =3D SUM (E_i*v_i) + SUM_ij(r_ji*v_i* dE_j/dr_i) Here the force and energy terms for each atom i still depend on all surrounding atoms not just atom j. Thanks so much, Anton On 1 February 2010 19:05, pascal boulet pascal.boulet:-:univ-provence.fr wrote: > > Sent to CCL by: pascal boulet [pascal.boulet(!)univ-provence.fr] > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Anton Lopis, > > If I am right, you should always be able to calculate forces on the > atoms since MD algorithms rely on forces to move the atoms. Which > algorithm is DL-POLY implementing? The question is, what is the > expression for the forces that correspond to your EAM functional? > > Pascal > > > > Anton Lopis aslopis__gmail.com a =E9crit : >> Sent to CCL by: Anton Lopis [aslopis^^^gmail.com] Dear CCL Users, >> >> I wish to be able to compute Thermal Conductivity from Molecular >> Dynamics trajectories. It involves use of Green-Kubo and >> autocorrelation of the heat current/heat flux. (eg as in V. >> Tretiakov and S. Scandolo, J. Chem. Phys., Vol. 120, No. 8, 22 >> February 2004). >> >> However, I am modelling metal systems using the EAM (Embedded Atom >> Method) and not standard Pair Potentials. The determination of the >> heat flux appears to require individual force and potential energy >> contributions F_ij and phi_ij. These are the forces and energies >> for each ij pair of atoms, respectively. >> >> This analysis would be relatively easy to implement in the case of >> Pair Potentials, but the EAM forces and energies are not defined in >> =A0terms of individual atom pairs, but rather from an Embedding >> Function along with a pair potential. The Embedding Function for >> any particular atom is computed using the electron density >> contributions from all surrounding atoms. >> >> I am using DL_POLY2 for my EAM calculations, but the analysis >> method is of course general. >> >> Does anyone have any comments, ideas or suggestions please? These >> could be in terms of the theory, programs or other. >> >> I really appreciate your input, Anton Lopis >> >> >> >> -=3D This is automatically added to each message by the mailing >> script =3D- To recover the email address of the author of the >> message, please change the strange characters on the top line to >> the , sign. You can also look up the X-Original-From: line in the >> mail header.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/> >> >> > > - -- > Dr. pascal Boulet, computational chemist > Laboratoire Chimie Provence, UMR 6264 > University of Aix-Marseille I > Avenue Escadrille Normandie-Niemen > 13397 Marseille Cedex 20 > France > ********** > Tel. (+33) (0)491.63.71.17 > Fax. (+33) (0)491.63.71.11 > ********** > http://www.lc-provence.fr > http://allos.up.univ-mrs.fr/boulet > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAktnCcoACgkQNLjdBN1V75mXRwCgt+mPhmaySUPGPtHvjtEu4yUk > xnIAoLaMCxNZ2Wfu5EyrDl2e6pmo7Pxw > =3DswR8 > -----END PGP SIGNATURE----- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Feb 2 08:50:01 2010 From: "Verena_Gossen Verena_Gossen]![web.de" To: CCL Subject: CCL:G: Gaussian and gaussview compatibility Message-Id: <-41164-100202035240-7390-zx73J/9iNTKeB127QqyPhA()server.ccl.net> X-Original-From: Verena_Gossen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 02 Feb 2010 09:19:24 +0100 MIME-Version: 1.0 Sent to CCL by: Verena_Gossen [Verena_Gossen ~~ web.de] Hi all, I currently use Gaussian09 with the older Gaussview 4.1.2 and have problems to calculate a ecd-spectra with the td-dft method. Whenever I try this, only a UV-spectra is shown in Gaussview. Does anyone know how to solve this problem? Thanks, Verena Gossen. From owner-chemistry@ccl.net Tue Feb 2 09:25:01 2010 From: "steinbrt[#]rci.rutgers.edu" To: CCL Subject: CCL: Announcement: Amber Molecular Dynamics Workshop 2010 at Duesseldorf, Germany Message-Id: <-41165-100202062218-7439-+IUk4gajK2KHf0bqgDy4jw^server.ccl.net> X-Original-From: steinbrt_._rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 2 Feb 2010 05:50:30 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: steinbrt-$-rci.rutgers.edu Dear colleagues, we are pleased to officially announce that the 2010 Amber MD Workshop at Duesseldorf university, Germany will take place from April 26-30. This five day course aims at providing a comprehensive overview over the Amber programs, with special consideration on new developments in Amber 11. The Amber suite of programs is one of the main molecular mechanics packages in use in the academic world, used by hundreds of scientists and actively developed by a loose community of professionals centered around Prof. David Case at Rutgers University. The group of Holger Gohlke at Duesseldorf university is hosting the event, with Ross Walker and Thomas Steinbrecher as lecturers. We have organized several international Amber workshops in the last years and are confident that this will again be a great opportunity for participants to enter the field of molecular simulation. The workshop is conceptually divided into a two day introductory and a three day advanced section. Participants will combine lectures, hands-on sessions and scientific case studies to get experience on how to conduct their own research projects using the Amber suite. The two goals are to provide new users with the ability to plan and conduct independent simulations, as well as introduce good practices on how to use some of the more advanced program features in scientific studies. The workshop homepage with registration forms, preliminary program and travel advisory can be found here: http://cpclab.uni-duesseldorf.de/workshop2010 Registration will be free, but participants have to arrange their own travel. We have approximately 25 participant slots available which will be filled on a first come, first serve basis. If you plan on attending, please register early as slots usually fill up fast. Please feel free to forward this announcement to others. Kind Regards, on behalf of the organizing team, Dr. Thomas Steinbrecher Universität Karlsruhe Inst. f. phys. Chemie 76131 Karlsruhe, Germany phone ++49 721 608 5703 From owner-chemistry@ccl.net Tue Feb 2 15:07:00 2010 From: "Joy Ku joyku|stanford.edu" To: CCL Subject: CCL: Developing Molecular Dynamics Algorithms on GPUs+Intro to MD Workshops Message-Id: <-41166-100202145136-5397-vIWXtALq11HKvK9kGOehSg---server.ccl.net> X-Original-From: "Joy Ku" Date: Tue, 2 Feb 2010 14:51:32 -0500 Sent to CCL by: "Joy Ku" [joyku|a|stanford.edu] Simbios is excited to announce its upcoming Molecular Dynamics (MD) Workshop Series, highlighting new capabilities within the recently released OpenMM 1.0 and introducing PyOpenMM for rapid MD code development with high performance: Day 1: Running and Developing MD Algorithms on GPUs with OpenMM Day 2: Introduction to MD and Trajectory Analysis with Markov State Models When: March 1-2, 2010 (sign up for one or two days) Where: Stanford University, Stanford, California Registration is free but required and spaces are limited. Visit http://simbios.stanford.edu/MDWorkshops.htm. ________________________________________________________________________ DAY 1: Running and Developing MD Algorithms on GPUs with OpenMM For those interested in running MD simulations on graphics processing units (GPUs) and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. Some programming background is required. Learn to: - Set up simulations using OpenMM (http://simtk.org/home/openmm), a freely downloadable library that enables MD simulations to run on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on GPUs. - Use OpenMM's custom force options to design and test new MD algorithms - Use PyOpenMM (http://simtk.org/home/pyopenmm), the Python version of OpenMM that is ideal for rapid code development but still achieves high performance DAY 2: Introduction to MD and Trajectory Analysis with Markov State Models For researchers (including novices to MD) interested in using MD and/or analyzing MD results in their research. During the workshop, you will: - Learn the theory behind MD - Use the OpenMM Zephyr (http://simtk.org/home/zephyr) application to easily run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs. - Learn different techniques for analyzing MD simulations, including Markov State Models and why they are suitable for this - Gain hands-on experience with the MSMBuilder software[3] (http://simtk.org/home/msmbuilder) to automatically construct Markov State Models for trajectory analysis OpenMM, OpenMM Zephyr, PyOpenMM, and MSMBuilder are supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures, as part of its protein folding research efforts. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu. [1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. [2]Eastman, P. and Pande, V.S. (2009). Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit. Journal of Computational Chemistry. (In press) [3] GR Bowman, X Huang, and VS Pande, "Using generalized ensemble simulations and Markov state models to identify conformational states," Methods, 49(2):197-201. From owner-chemistry@ccl.net Tue Feb 2 16:41:01 2010 From: "pascal boulet pascal.boulet{=}univ-provence.fr" To: CCL Subject: CCL: Computing Thermal Conductivity Message-Id: <-41167-100202163707-18707-SE5vIe2fZTIwunGaKuFXgA[#]server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 02 Feb 2010 22:00:10 +0100 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet!^!univ-provence.fr] -----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello,

Well, of course I understand the problem of the manybody potential.
But, have you tried to use the forces as they are given in the output
of DLPOLY? Do you obtain a thermal conductivity that is very different
> from what you expect?

As far as I understand the Green-Kubo formula, it does not say how
j(t) should be calculated.

Maybe this document can help you:
http://www.wag.caltech.edu/events/cmdf/CMDF%28050823%29%20-%20Oyafuso,%20Fabiano%20-%20Thermal%20Conductivity%20Calculations.pdf

Pascal

Anton Lopis aslopis[-]gmail.com a écrit :
> Sent to CCL by: Anton Lopis [aslopis^^gmail.com] Hi Pascal,
>
> Thanks for the reply and suggestion Pascal, appreciate it.
>
> Yes, DL_POLY2 (2.18) does of course calculate the forces for each
> atom and can write them in the trajectory (history) file.
> Unfortunately these do not appear to be the forces - or energies -
> required for thermal conductivity analysis.
>
> DL-POLY yields the forces on each atom due to all the other atoms
> (from the gradient of the potential). What I believe I require is
> forces F_ij, that is the forces on atom i due to only atom j. It is
> the Embedding function which causes the complications - since it
> depends on all the surrounding atoms (via the electron density
> contributions), not just atom j. Energy contributions are also
> complicated in this way.
>
> The same issues remain if one reformulates the current density j: j
> = d/dt (SUM E_i*r_i) = SUM (E_i*v_i) + SUM_ij(r_ji*v_i* dE_j/dr_i)
> Here the force and energy terms for each atom i still depend on all
> surrounding atoms not just atom j.
>
> Thanks so much, Anton
>
>
> On 1 February 2010 19:05, pascal boulet
> pascal.boulet:-:univ-provence.fr <owner-chemistry * ccl.net> wrote:
>
>> Sent to CCL by: pascal boulet [pascal.boulet(!)univ-provence.fr]
> Dear Anton Lopis,
>
> If I am right, you should always be able to calculate forces on the
> atoms since MD algorithms rely on forces to move the atoms. Which
> algorithm is DL-POLY implementing? The question is, what is the
> expression for the forces that correspond to your EAM functional?
>
> Pascal
>
>
>
> Anton Lopis aslopis__gmail.com a écrit :
>>>> Sent to CCL by: Anton Lopis [aslopis^^^gmail.com] Dear CCL
>>>> Users,
>>>>
>>>> I wish to be able to compute Thermal Conductivity > from
>>>> Molecular Dynamics trajectories. It involves use of
>>>> Green-Kubo and autocorrelation of the heat current/heat flux.
>>>> (eg as in V. Tretiakov and S. Scandolo, J. Chem. Phys., Vol.
>>>> 120, No. 8, 22 February 2004).
>>>>
>>>> However, I am modelling metal systems using the EAM (Embedded
>>>> Atom Method) and not standard Pair Potentials. The
>>>> determination of the heat flux appears to require individual
>>>> force and potential energy contributions F_ij and phi_ij.
>>>> These are the forces and energies for each ij pair of atoms,
>>>> respectively.
>>>>
>>>> This analysis would be relatively easy to implement in the
>>>> case of Pair Potentials, but the EAM forces and energies are
>>>> not defined in terms of individual atom pairs, but rather
>>>> from an Embedding Function along with a pair potential. The
>>>> Embedding Function for any particular atom is computed using
>>>> the electron density contributions from all surrounding
>>>> atoms.
>>>>
>>>> I am using DL_POLY2 for my EAM calculations, but the analysis
>>>> method is of course general.
>>>>
>>>> Does anyone have any comments, ideas or suggestions please?
>>>> These could be in terms of the theory, programs or other.
>>>>
>>>> I really appreciate your input, Anton Lopis
>>>>
>>>>
>>>>
>>>> -= This is automatically added to each message by the mailing
>>>> script =- To recover the email address of the author of the
>>>> message, please change the strange characters on the top line
>>>> to the , sign. You can also look up the X-Original-From: line
>>>> in the mail
>>>> header.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
>>>> http://server.ccl.net/chemistry/announcements/conferences/>
>>>>
>>>>
>>
>>
>>
- -= This is automatically added to each message by the mailing script
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>>

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- --
Dr. pascal Boulet, computational chemist
Laboratoire Chimie Provence, UMR 6264
University of Aix-Marseille I
Avenue Escadrille Normandie-Niemen
13397 Marseille Cedex 20
France
**********
Tel. (+33) (0)491.63.71.17
Fax. (+33) (0)491.63.71.11
**********
http://www.lc-provence.fr
http://allos.up.univ-mrs.fr/boulet
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From owner-chemistry@ccl.net Tue Feb 2 17:58:01 2010 From: "Ron Bakus rbakus!^!chem.ucsb.edu" To: CCL Subject: CCL:G: Optimization getting stuck, with no further improvements Message-Id: <-41168-100202171828-21448-B3NBcWbz8mxnSOEpBNuh6w~~server.ccl.net> X-Original-From: "Ron Bakus" Date: Tue, 2 Feb 2010 17:18:24 -0500 Sent to CCL by: "Ron Bakus" [rbakus~!~chem.ucsb.edu] Im trying to optimize a pi complex involving a phosphine ligated palladium bound to an aryl ring, and the optimization proceeds through scf cycles just fine, and then it reaches a point where it is predicting a large change in energy (-8Hartree) for the next scf cycle, but there is no further change in the energy (or the predicted change) or convergence, even after 10 additional scf cycles have completed (each scf cycle converges just fine). Has anyone seen this before, and if so, is there an easy way to deal with the problem? Sample output below: Item Value Threshold Converged? Maximum Force 0.016811 0.000450 NO RMS Force 0.001742 0.000300 NO Maximum Displacement 0.077557 0.001800 NO RMS Displacement 0.011014 0.001200 NO Predicted change in Energy=-8.338644D+00 (I stopped counting the number of scf cycles that outputted this at 10). Software/Basis: G03 03.E, organic bits 6-31+G(d,p), P Lanl08(d), and Pd Lanl08(f). Route: #p opt b3lyp/genecp geom=connectivity formcheck PS. I'm thinking of trying int=ultrafine to see if this fixes this issue, but I'm looking for other suggested solutions. Thanks Ron Bakus