From owner-chemistry@ccl.net Tue Apr 22 00:26:00 2014 From: "Tian Lu sobereva=-=sina.com" To: CCL Subject: CCL: NCIPLOT Message-Id: <-49949-140422000210-20674-uW8tJsodiG5mKwm9lWnHFA.:.server.ccl.net> X-Original-From: "Tian Lu" Date: Tue, 22 Apr 2014 00:02:09 -0400 Sent to CCL by: "Tian Lu" [sobereva _ sina.com] Hi, A more ideal way to carry out the NCI analysis is using Multiwfn (http://multiwfn.codplex.com, JCC,33,580). Multiwfn generates the grid data quite fast, the grid range and spacing can be conveniently set in an interactive interface, and the RDG isosurface as well as the scatter map of RDG vs sign(lambda_2)rho can be plotted in Multiwfn directly. If it is used in combination with the freeware VMD, very nice sign(lambda_2)rho mapped RDG isosurfaces can be readily drawn. Please check Section 4.100.1 of the Multiwfn manual for example, the script used in VMD is also provided. As you are a GAMESS (US) user, the input file you need to provide to Multiwfn is the .wfn file generated by AIMPAC=.TRUE. keyword. Worthnotingly, Multiwfn is also able to perform NCI analysis for dynamic environment (namely multi-frames cases, such as MD trajectory), see Section 4.200.1 for example. Best wishes, Tian Lu ----- Original Message ----- > From: "darren.rhodes darren.rhodes{}gmail.com" To: "Lu, Tian " Subject: CCL: NCIPLOT Date: 2014-04-22 03:46 Hi All Further to the note below, Prof Rzepa's code found on figshare, http://figshare.com/articles/Generating_an_NCI_surface_using_Jmol/811862, can be used to generate NCI surfaces. Initially, as a GAMESS (US) user I found it difficult to use the code since it requires a Guassian cube file to work but GAMESS (US) has the capacity to generate a cube file. This is done using the $GRID keyword (see input.doc for details, I would recommend using a smaller grid increment, 0.1, than the default 0.25) with the output being found in the .dat file (usually found in the scratch directory, with keywords START OF CUBE FORMAT). I scraped the cube file data from the .dat file and placed it in a new text document which was imported into the Jmol script found on figshare. This worked for a water dimer indicating the hydrogen bond between the two molecules. I hope that this post is useful and if anyone wants to crib my input code, here it is, ! File created by the GAMESS Input Deck Generator Plugin for Avogadro $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $CONTRL SCFTYP=RHF RUNTYP=ENERGY $END $ELDENS IEDEN=1 WHERE=GRID $END $GRID MODGRD=1 ORIGIN(1)=1,4,1 XVEC(1)=-3,4,1 YVEC(1)=1,0,1 ZVEC(1)=1,4,-1 $END $GRID SIZE=0.1 $END $SYSTEM MWORDS=250 $END $DATA Water Dimer on a finer grid C1 O 8.0 -1.98478 0.93709 0.00591 H 1.0 -2.48259 0.88733 -0.84147 H 1.0 -1.34547 1.69675 -0.10169 O 8.0 -0.15225 2.97721 -0.02767 H 1.0 0.66933 2.48664 0.20669 H 1.0 -0.43068 3.46012 0.78453 $END Darren. From owner-chemistry@ccl.net Tue Apr 22 01:54:00 2014 From: "Rzepa, Henry S h.rzepa^_^imperial.ac.uk" To: CCL Subject: CCL: NCIPLOT Message-Id: <-49950-140422015210-22314-ICXfp5q6G3DIexKtMdO4OA#,#server.ccl.net> X-Original-From: "Rzepa, Henry S" Content-Language: en-US Content-Type: multipart/signed; boundary="Apple-Mail=_7C50AAC9-2D30-4C58-933D-179742600F7C"; protocol="application/pgp-signature"; micalg=pgp-sha512 Date: Tue, 22 Apr 2014 05:52:01 +0000 MIME-Version: 1.0 Sent to CCL by: "Rzepa, Henry S" [h.rzepa%imperial.ac.uk] --Apple-Mail=_7C50AAC9-2D30-4C58-933D-179742600F7C Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 On 21 Apr 2014, at 22:44, V=EDctor Lua=F1a Cabal victor a = fluor.quimica.uniovi.es wrote: >=20 > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal = [victor() fluor.quimica.uniovi.es] > On Mon, Apr 21, 2014 at 08:46:56PM +0100, darren.rhodes = darren.rhodes{}gmail.com wrote: >> Hi All >>=20 >> Further to the note below, Prof Rzepa's code found on figshare, >> = http://figshare.com/articles/Generating_an_NCI_surface_using_Jmol/811862, >> can be used to generate NCI surfaces. >=20 > Why don't you try with the codes by the creators of NCI plots. Look = for > Erin Johnson in University of California at Merced, Julia Contreras in > Universit=E9 Pierre et Marie Curie de Paris, or Alberto = Otero-de-la-Roza > in the NINT, University of Edmonton. You will find freewares and > professional codes. >=20 > This is not to discard the explendid work by Rzepa. However, citing > the creators of the technology has clear advantages. >=20 Since my name has been mentioned, I should clarify the origins of the = above resource. Obtaining the NCI surface from a cube of electron = density values was implemented in the Open source program Jmol by Bob = Hanson, with the help of Julia Contreras. We have mounted a scripted = version of Jmol which performs this operation on Figshare. In fact, = anyone who acquires Jmol can do this for themselves (you will need the = Java version, which in this regard is very much faster than JSmol.) --Apple-Mail=_7C50AAC9-2D30-4C58-933D-179742600F7C Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="signature.asc" Content-Type: application/pgp-signature; name="signature.asc" Content-Description: Message signed with OpenPGP using GPGMail -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: GPGTools - https://gpgtools.org iQEcBAEBCgAGBQJTVgN/AAoJEO1XNzHjQU1W4iUH/3Gb3QP3F/yjnYbF5Rosd0cj uYsgbVoJ+Zinuc/UfGaQkf7/J9SYMAIrDjk59dV47P3PhZF9eral88VXvfi/uVw8 qWq6olQIf/9vdFkO+h0c/1bdIKYETiUgrD/q8k41rA+h5RwmQhC8BNF/w8fSWgjc Js8kHNB7siHFxwPmhiANTPHMyV+GuxhI+q5sqFfsV9SfrxZLgg4Bh2KviZHGY0RS Wgx2jgq1AoJZcuTlBXGjtrsdS2Hz0mWM4CTjXFEpFNasmrgymlWhL7mYNy4uZ05M G78/bhyPV6gdUehCpdyYSHLUhiFFrAQ1TJDcRjae/vm5l7iHQ7NsU5V/TZKCF9s= =f7H9 -----END PGP SIGNATURE----- --Apple-Mail=_7C50AAC9-2D30-4C58-933D-179742600F7C-- From owner-chemistry@ccl.net Tue Apr 22 10:14:00 2014 From: "Hanna Thamleena hannathamleena*gmail.com" To: CCL Subject: CCL: how to generate MEP for oniom calculations ? Message-Id: <-49951-140422085403-7126-XkVvko+N4sBQ+5McTisWnA===server.ccl.net> X-Original-From: Hanna Thamleena Content-Type: multipart/alternative; boundary=001a1133f890ffdfd304f7a11be3 Date: Tue, 22 Apr 2014 18:23:58 +0530 MIME-Version: 1.0 Sent to CCL by: Hanna Thamleena [hannathamleena,+,gmail.com] --001a1133f890ffdfd304f7a11be3 Content-Type: text/plain; charset=UTF-8 I want to generate an electrostatic potential map for a two layer oniom geometry optimization calculation. When I opened the formchk file in GaussView the surfaces/contours option was found to be inactive while the charge distribution option was active. How can I produce the potential map? Hanna Thamleena Research Scholar National institute of Technology Calicut INDIA --001a1133f890ffdfd304f7a11be3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I want to generate an electrostatic potential map for= a two layer oniom geometry optimization calculation. When I opened the for= mchk file in GaussView the =C2=A0surfaces/contours option was found to be i= nactive while the charge distribution option was active. How can I produce = the potential map?





=
Hanna Thamleena
Research Schola= r
National institute of Technology Calicut
INDIA
<= /div>
--001a1133f890ffdfd304f7a11be3-- From owner-chemistry@ccl.net Tue Apr 22 13:39:00 2014 From: "=?UTF-8?Q?Serdar_Bado=C4=9Flu?= serdarbadoglu###gmail.com" To: CCL Subject: CCL: how to generate MEP for oniom calculations ? Message-Id: <-49952-140422133626-9029-af2QHl5My/Co8vNXzGQpcA]_[server.ccl.net> X-Original-From: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= Content-Type: multipart/alternative; boundary=089e0158a836cda5bc04f7a50dae Date: Tue, 22 Apr 2014 20:36:20 +0300 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= [serdarbadoglu---gmail.com] --089e0158a836cda5bc04f7a50dae Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Hanna, You may want to see this link: http://staff.ycp.edu/~jforesma/educ/visual/index.html On Tue, Apr 22, 2014 at 3:53 PM, Hanna Thamleena hannathamleena*gmail.com < owner-chemistry() ccl.net> wrote: > I want to generate an electrostatic potential map for a two layer oniom > geometry optimization calculation. When I opened the formchk file in > GaussView the surfaces/contours option was found to be inactive while th= e > charge distribution option was active. How can I produce the potential ma= p? > > > > > > > Hanna Thamleena > Research Scholar > National institute of Technology Calicut > INDIA > --=20 Serdar BADO=C4=9ELU, Ph.D. Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC --089e0158a836cda5bc04f7a50dae Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Hanna,

You may want to see this link= :=C2=A0ht= tp://staff.ycp.edu/~jforesma/educ/visual/index.html


On Tue, Apr 22, 2014 at 3:53 PM, Hanna T= hamleena hannathamleena*gmail.com <= owner-chemistry() ccl.net> wrote:
I want to generate an = electrostatic potential map for a two layer oniom geometry optimization cal= culation. When I opened the formchk file in GaussView the =C2=A0surfaces/co= ntours option was found to be inactive while the charge distribution option= was active. How can I produce the potential map?





=
Hanna Thamleena
Research Schola= r
National institute of Technology Calicut
INDIA



--
Serdar BADO= =C4=9ELU, Ph.D.
Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC
--089e0158a836cda5bc04f7a50dae--