From owner-chemistry@ccl.net Mon May 8 03:19:00 2017 From: "=?UTF-8?Q?Bj=c3=b6rn_Sommer?= bjoern[-]CELLmicrocosmos.org" To: CCL Subject: CCL: CELLmicrocosmos MembraneEditor: Quad-2 Release Message-Id: <-52790-170507153552-23895-Kn5tvvLo2yEB7J+OeKym0Q[]server.ccl.net> X-Original-From: =?UTF-8?Q?Bj=c3=b6rn_Sommer?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Sun, 7 May 2017 21:35:44 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Bj=c3=b6rn_Sommer?= [bjoern(_)CELLmicrocosmos.org] Hi all! We are happy to announce the Quad-2 Release of the CELLmicrocosmos MembraneEditor! The most important change is the substitution of the old Oracle Java 3D libraries by JogAmp's Java 3D 1.6.0 implementation. Now the 3D visualization is faster, more reliable, and we can support now Mac OS X! Many thanks go to the whole JogAmp team for their support! Second, the Web Start was re-initiated and optimized for Java 8, running on all major platforms including Mac OS X! Then, Stereo 3D visualization is fully supported now. There is an extra version for professional graphics and 3D devices, but also the standard version is coming with side-by-side or top-bottom rendering for, e.g., 3D-TVs (sorry, does not work on Mac). Moreover, we fixed the PDBTM update – as there was a new website release of PDBTM, the update functionality for the membrane placement matrices was broken. Now, you have again full support for automatic protein placement! More details below! To start over, just go to: http://Cm2.CELLmicrocosmos.org Vive la France! ;-) Bjorn The Quad-2 Release: JogAmp's Java3D Update, Stereoscopic 3D Update, PDBTM Bugfix, Java Web (Re)Start version 2.2.2_2 (07.05.2017) - JogAmps JOGL-based Java 3D 1.6.0 implementation with a special fix by Phil enables MembraneEditor now on Linux, Windows, and !NEW! Mac OS X Moreover, Java3D is now faster and more reliable than before! (Java3D Version: 1.6.0-experimental pj1, based on 1.6.0-final) (JOGL version: 2.3.2) Thanks go to Julien, Harvey and Phil from JogAmp for developing their Java3D continuation - new OPM and PDBTM Update Description files included in cm2settings (opm.mif and pdbtm.mif) - PDBTM Update Functionality fixed - URL changed and XML files provided by PDBTM are not XML conform, file is fixed now before parsing - Stereoscopic 3D side-by-side or top/bottom functionality for consumer 3D TVs etc. added (disabled on Mac OS X, does currently not work) - tools.jar from JDK8u25 added - Compilation of Java files should be only possible with Java 8 now. - Re-initiated Java Web Start with Linux, Windows and Mac OS X support - Now added a version for Stereoscopic 3D support for professional graphics for Java Web Start Full update history here: http://www.cellmicrocosmos.org/index.php/cm2help/11-more-about-the-editor/11-5-history From owner-chemistry@ccl.net Mon May 8 09:20:00 2017 From: "Mehboob Alam mehboob.cu|-|gmail.com" To: CCL Subject: CCL:G: Solvent Message-Id: <-52791-170508052950-1184-61ExEcgEI6Yy2M6+alOZKA\a/server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=94eb2c0eb82c14132b054effe1eb Date: Mon, 8 May 2017 11:29:03 +0200 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu^^gmail.com] --94eb2c0eb82c14132b054effe1eb Content-Type: text/plain; charset=UTF-8 Hello, Xylene is already in the solvent list. So, you can just use scrf=(solvent=o-xylene), if your solvent is o-xylene. If your solvent is m-xylene or p-xylene, use scrf=(solvent=m-xylene) or scrf=(solvent=p-xylene) respectively. If your solvent is a mixture of the three then use scrf=(solvent=xylene-mixture). Hope it helps. Best wishes, Mehboob Dr. Md. Mehboob Alam Post-Doctoral Researcher Department of Chemistry UiT The Arctic University of Norway PostDoc Supervisor - Prof. Kenneth Ruud On Sun, May 7, 2017 at 1:18 PM, Elvis Martis elvis_bcp_._elvismartis.in < owner-chemistry!A!ccl.net> wrote: > you can instead use the keywords > scrf=(solvent=generic,read) > and in the additional keyword add the dielectric of o-xylene as > "EPS=2.57" without quotes > Please refer this chart for Dielectric constants > > Best Regards > [image: photo] > > Elvis Martis > Ph.D. Student (Computational Chemistry) > at Bombay College of Pharmacy > A Kalina, Santacruz [E], Mumbai 400098, INDIA > W www.elvismartis.in > Skype. adrian_elvis12 > > > > On 7 May 2017 at 15:18, Mina Haghdadi mhaghdadi2!^!yahoo.co.uk < > owner-chemistry:ccl.net> wrote: > >> >> Sent to CCL by: Mina Haghdadi [mhaghdadi2{=}yahoo.co.uk] >> >> Dear all >> I would like calculate some molecules in solvent ( xylene) by Gaussian >> but it (xylene) is not at the keywords of gauss view . Could you help me >> what is keyword ? for example in H2o it is :scrf=(solvent=H2O) >> Thank you >> Mina >> Sent from my iPhone>> E-mail to subscribers: CHEMISTRY:ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST:ccl.net or use>> >> >> > --94eb2c0eb82c14132b054effe1eb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello,

Xylene is already in the solvent= list. So, you can just use=C2=A0scrf=3D(solvent=3Do-xylene), if your solvent is o-xylene.
=
If your solvent is m-xy= lene or p-xylene, use=C2=A0scrf=3D(solvent=3Dm-xylene) or=C2=A0scrf=3D(solvent=3Dp-xylene) respectively. If your solv= ent is a mixture of the three then use=C2=A0scrf=3D(solvent=3Dxylene-mixture).
=
Hope it helps.

Best wishes,
Mehboob

Dr. Md. Mehboob Alam
Post-Doctoral Researcher
Department of Chemistry
U= iT The Arctic University of Norway
PostDoc Supervisor - Prof. Kenneth Ruud

On Sun, May 7, 2017 at 1:18 PM, Elvis Martis= elvis_bcp_._elvismartis.in <o= wner-chemistry!A!ccl.net> wrote:
you can instead use the keywords
scrf=3D(solven= t=3Dgeneric,read)
and in the additional keyword add the dielectric of= o-xylene as
"EPS=3D2.57" without quotes
Please refer= this chart for Dielectric constants
=
<= div dir=3D"ltr">
=C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
=C2= =A0at=C2=A0Bombay College of Pharmacy
A=C2=A0=C2= =A0Kalina, Santacruz [E], Mumbai 400098, INDIA
W=C2=A0= www.elvismartis.inSkype.=C2=A0adrian_elvis1= 2


On 7 May 2017 at 15:18, Min= a Haghdadi mhaghdadi2!^!ya= hoo.co.uk <owner-chemistry:ccl.net> wrote:

Sent to CCL by: Mina Haghdadi [mhaghdadi2{=3D}yahoo.co.uk]

Dear all
I would like calculate some molecules in solvent ( xylene) by Gaussian but = it (xylene) is not at the keywords of gauss view . Could you help me what= =C2=A0 is keyword ? for example in H2o it is :scrf=3D(solvent=3DH2O)
Thank you
Mina
Sent from my iPhone



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY:ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST:ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/s= ub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutcc= l/instructions/




--94eb2c0eb82c14132b054effe1eb--