From owner-chemistry@ccl.net Wed Jul 2 11:06:00 2014 From: "Andras Borosy andras.borosy[]givaudan.com" To: CCL Subject: CCL: NAMD vs GROMACS? Message-Id: <-50302-140702102054-19571-m839QZPlYWvEolF0r2bfLQ=-=server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 004ECE73C1257D09_=" Date: Wed, 2 Jul 2014 16:20:46 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy%a%givaudan.com] This is a multipart message in MIME format. --=_alternative 004ECE73C1257D09_= Content-Type: text/plain; charset="US-ASCII" Dear Colleagues, I wish to run MD simulations by using a relatively small host system (with a small organic guest molecule) in batch mode at a parallel RedHat linux computer. NAMD vs GROMACS (or anything else) would be better for a novice? Many thanks, Andras Borosy --=_alternative 004ECE73C1257D09_= Content-Type: text/html; charset="US-ASCII" Dear Colleagues,

I wish to run MD simulations by using  a relatively small host  system (with a small organic guest molecule) in batch mode at a parallel RedHat linux computer. NAMD vs GROMACS (or anything else) would be better for a novice?

Many thanks,

Andras Borosy


--=_alternative 004ECE73C1257D09_=-- From owner-chemistry@ccl.net Wed Jul 2 12:47:00 2014 From: "Italo Anjos italocurvelo/./gmail.com" To: CCL Subject: CCL: Is there a good program to calculate ellipticity profiles? Message-Id: <-50303-140702124324-23249-T79+31KDHsUPoTN12efp0w.:.server.ccl.net> X-Original-From: Italo Anjos Content-Type: multipart/alternative; boundary=20cf303349b1f371b804fd3896fc Date: Wed, 2 Jul 2014 13:43:19 -0300 MIME-Version: 1.0 Sent to CCL by: Italo Anjos [italocurvelo-,-gmail.com] --20cf303349b1f371b804fd3896fc Content-Type: text/plain; charset=UTF-8 Hi all, I've been running some QTAIM calculations and I would like to calculate ellipticity profiles along bond paths. Does anyone know a software which can perform such calculations? I usually make use of AIMAll package but the software seems unable to calculate ellipticity profiles. I appreciate any help. With regards, Italo --20cf303349b1f371b804fd3896fc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi all,

I've been running some QTAI= M calculations and I would like to calculate ellipticity profiles along bon= d paths. Does anyone know a software which can perform such calculations?= =C2=A0

I usually make use of AIMAll package but the software s= eems unable to calculate ellipticity profiles.

I a= ppreciate any help.

With regards,

Italo


--20cf303349b1f371b804fd3896fc-- From owner-chemistry@ccl.net Wed Jul 2 19:41:00 2014 From: "Tian Lu sobereva+/-sina.com" To: CCL Subject: CCL: Is there a good program to calculate ellipticity profiles? Message-Id: <-50304-140702182353-3141-zObqYkGma+9CT/zTLZeCTQ{:}server.ccl.net> X-Original-From: "Tian Lu" Date: Wed, 2 Jul 2014 18:23:51 -0400 Sent to CCL by: "Tian Lu" [sobereva%x%sina.com] Dear Italo, You can use Multiwfn (http://multiwfn.codeplex.com) to do this. Below is a simple example, we calculate and plot ellipicity of electron density along bond path of C-F in C2H5F. After extract Multiwfn package, first open settings.ini file and change "iuserfunc" parameter to 30 (The 30th user-defined function corresponds to electron density ellipicity, see Section 2.7 of the manual for detail). Then boot up Multiwfn and input below commands: examples\c2h5f.wfn 2 // Topology analysis 2 // Search NCP from nuclear positions 3 // Search BCP from midpoint of atom pairs 8 // Generate bond path 0 // Enter GUI window to visualize result In the GUI window, by using "Atom labels" and "Path labels" widgets at right side, we find paths 9 and 10 collectively correspond to the bond path of C-F. Clicking "RETURN" to close the window, and input -5 7 // Calculate specific real space funtion along a path 9,10 // The index of the paths 100 // User-defined function, which corresponds to ellipicity of electron density currently The curve of electron density ellipicity along the C-F bond path immediately shows on the screen, the dash line denotes the position of BCP. At the same time, the raw data of the curve are shown on the command-line window and you may copy them out. For more information about the topology analysis module of Multiwfn you can consult Section 3.14 of the manual and the examples in Section 4.2. PS: By using main functions 3 and 4 of Multiwfn, the electron density ellipicity can also be easily plotted in a line or in a plane. Best wishes, Tian Lu Beijing Kein Research Center for Natural Sciences, Beijing, P. R. China mailto: sobereva(_)sina.com ----- Original Message ----- > From: "Italo Anjos italocurvelo/./gmail.com" To: "Lu, Tian " Subject: CCL: Is there a good program to calculate ellipticity profiles? Date: 2014-07-03 00:43 Hi all, I've been running some QTAIM calculations and I would like to calculate ellipticity profiles along bond paths. Does anyone know a software which can perform such calculations? I usually make use of AIMAll package but the software seems unable to calculate ellipticity profiles. I appreciate any help. With regards, Italo