From owner-chemistry@ccl.net Thu Oct 7 16:34:01 2010 From: "Shina Caroline Lynn Kamerlin skamerli()usc.edu" To: CCL Subject: CCL: Frontiers in the Simulation of Macromolecules, LA, Nov 12-14 Message-Id: <-42917-101007163022-16526-VHboCs/mhQEb1YM7a1hs/Q:server.ccl.net> X-Original-From: "Shina Caroline Lynn Kamerlin" Date: Thu, 7 Oct 2010 16:30:13 -0400 Sent to CCL by: "Shina Caroline Lynn Kamerlin" [skamerli-*-usc.edu] Dear all, As you are aware, the simulation of biological function has advanced enormously since the early attempts to understand how biological systems work. The emergence of effective approaches, the increase in computational power, and a rapid expansion of the field have allowed for the simulation of ever more challenging biological problems. A symposium marking both the landmarks and the current frontiers in the field of molecular simulation will be held at the University of Southern California between the 12th and 14th of November. Confirmed invited speakers include Rudy Marcus, Harry Gray, Michael Levitt and Peter Wolynes, amongst others. I apologize for the late email - unfortunately, the oral presentation slots are currently full. However, there is still the possibility to present a poster, should you be interested. More detailed information about our symposium can be found at: https://michele.usc.edu/FSM2010/ And, should you have any queries, you can reach me directly at skamerli [at] usc.edu. Best regards, Lynn Kamerlin From owner-chemistry@ccl.net Thu Oct 7 17:20:00 2010 From: "Jamin Krinsky jamink{}berkeley.edu" To: CCL Subject: CCL:G: CH3I ground state calculation Message-Id: <-42918-101007171849-29135-9ah6FTAGxNhUASNuchiZYQ!=!server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 7 Oct 2010 14:18:36 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink**berkeley.edu] Hi Henry, Your example input looks just fine, is it not running correctly? Keep in mind that specifying that basis set makes the program use the D95V basis for H and first-row atoms, and second row (P, S, Cl, etc) atoms do not get polarization functions. You may want to only use LANL2DZ for your iodine, and a Pople basis set like 6-31G(d,p) for everything else (through Cl at least). Here is an example input: %chk=ch3i2.chk %nproc=2 %mem=120MW # opt freq b3lyp/gen pseudo=read ch3i 0 1 c i 1 ic2 h 1 hc3 2 hci3 h 1 hc4 2 hci4 3 dih4 h 1 hc5 2 hci5 4 dih5 variables ic2 2.099967 hc3 1.070016 hci3 109.473 hc4 1.070016 hci4 109.473 dih4 120.011 hc5 1.070000 hci5 109.469 dih5 119.995 c h 0 6-31G(d,p) **** i 0 lanl2dz **** i 0 lanl2dz {at least one blank line here!!!} Note that in your route (keyword) section there is "gen" instead of the basis name, and an additional keyword stating that the input stream contains a pseudopotential (ECP) section. Below the molecular specification (after a blank line) is the basis section (the 0s after the atoms are zeros, not oxygen, and they are always needed), then after another blank line is what looks like a repeat for iodine but is actually the pseudopotential section. Make sure there is at least one blank line at the end of your input file. Hope this helps, Jamin On Wed, Oct 6, 2010 at 5:30 PM, Henry Martinez hmartine[-]gmail.com wrote: > > Sent to CCL by: "Henry  Martinez" [hmartine!^!gmail.com] > I am trying to calculate the ground state of CH3I using LANL2DZ as a basis set, but I wan to use the Electron core potential (ECP) for the Iodine. However, I have no idea how to do it. The input should have some extras, even I read Gaussian manual, I do not really see how this input should go. Can anybody help me with this? > > %chk=ch3i2.chk > %nproc=2 > %mem=120MW > # opt freq b3lyp/LANL2DZ > > ch3i > > 0 1 >  c >  i   1 ic2 >  h   1 hc3        2 hci3 >  h   1 hc4        2 hci4         3 dih4 >  h   1 hc5        2 hci5         4 dih5 > variables > ic2         2.099967 > hc3         1.070016 > hci3        109.473 > hc4         1.070016 > hci4        109.473 > dih4        120.011 > hc5         1.070000 > hci5        109.469 > dih5        119.995>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Oct 7 21:28:00 2010 From: "neranjan perera neranjan007(0)gmail.com" To: CCL Subject: CCL:G: G03 checkpoint file of ONIOM Message-Id: <-42919-101007212638-9992-BRink3/013M4xDPeIkHXUg..server.ccl.net> X-Original-From: neranjan perera Content-Type: multipart/alternative; boundary=001636c5a2ab82592b049210e6ad Date: Thu, 7 Oct 2010 21:26:31 -0400 MIME-Version: 1.0 Sent to CCL by: neranjan perera [neranjan007(0)gmail.com] --001636c5a2ab82592b049210e6ad Content-Type: text/plain; charset=ISO-8859-1 Hi , I would also like to add some more to the question. I did an ONIOM calculation and tried to format the chk file, and then used to cubegen to generate the cube files which was used to get the charge density of the system, but it only produced the charge density for the QM part, it did not gave any charge for the MM part. Is there a way to get the charge density of the MM part of the system when doing a ONIOM calculation. Thank you so much Neranjan Perera On Mon, Oct 4, 2010 at 8:27 AM, bobby sitayya{:}gmail.com < owner-chemistry__ccl.net> wrote: > Dear, > You need to increase the default GAUSS_MEMDEF size for formatting the > checkpoint of ONIOM file > if you are on linux/max you should change the GAUSS_MEMDEF environment > variable (ex. if you are in C shell, you should use > setenv GAUSS_MEMDEFF 4000MB ) > > That should solve the problem. > If not give more details of what you did and your output file. > > > > > > > On Mon, Oct 4, 2010 at 5:46 AM, Miko Felix mfx=mmqc.org < > owner-chemistry~!~ccl.net > wrote: > >> >> Sent to CCL by: "Miko Felix" [mfx(-)mmqc.org] >> Dear CCLers, >> >> has anyone ever tried to get the formatted checkpoint file in G03 out of >> the >> ONIOM calculation? The following command: >> >> GAUSS_MEMDEF=9000000 formchk pro-ext-recalc.gjf.chk >> pro-ext-recalc.gjf.fchk >> >> gives in the output only MM-part. (GAUSS_MEMDEF is required, otherwise >> formchk will segfault) >> >> The header then looks like this: >> >> .. >> FOpt ONIOM(B3LYP/6-31G(d):AMBER/ZDO) >> Mixed >> Number of atoms I 2048 >> Charge I 0 >> Multiplicity I 2 >> Number of electrons I 0 >> Number of alpha electrons I 0 >> Number of beta electrons I 0 >> Number of basis functions I 0 >> Number of independant functions I 0 >> Number of point charges in /Mol/ I 0 >> Number of translation vectors I 0 >> >> How do I get the formatted checkpoint file with the QM-region inside? I >> could not find any information nor hints in Gaussian manual. >> >> Thanks, MFX>> E-mail to subscribers: CHEMISTRY~!~ccl.net or >> use:>> >> E-mail to administrators: CHEMISTRY-REQUEST~!~ccl.netor use>> >> >> > --001636c5a2ab82592b049210e6ad Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi ,
=A0 I would also like to add some more to the question.

I di= d an ONIOM calculation and tried to format the chk file, and then used to c= ubegen to generate the cube files which was used to get the charge density = of the system, but it only produced the charge density for the QM part, it = did not gave any charge for the MM part. Is there a way to get the charge d= ensity of the MM part of the system when doing a ONIOM calculation.

Thank you so much


Neranjan Perera





On Mon, Oct 4, 2010 at 8:27 AM, bobby sitayya{:}gmail.com <owner-chemistry__ccl.net> wrote= :
Dear,
You nee= d to increase the default GAUSS_MEMDEF size for formatting the checkpoint o= f ONIOM file
if you are on linux/max you should change the GAUSS_MEMDEF environment vari= able (ex. if you are in C shell, you should use
setenv GAUSS_MEMDEFF 4000MB )

That should solve the problem.
If = not give more details of what you did and your output file.



=


On Mon, Oct 4, 201= 0 at 5:46 AM, Miko Felix mfx=3Dmmqc.org <owner-chemistry~!~ccl.net> wro= te:

Sent to CCL by: "Miko =A0Felix" [mfx(-)mmqc.org]
=A0Dear CCLers,

=A0has anyone ever tried to get the formatted checkpoint file in G03 out of= the
ONIOM calculation? The following command:

=A0GAUSS_MEMDEF=3D9000000 formchk pro-ext-recalc.gjf.chk pro-ext-recalc.gjf= .fchk

gives in the output only MM-part. (GAUSS_MEMDEF is required, otherwise
formchk will segfault)

The header then looks like this:

..
FOpt =A0 =A0 =A0ONIOM(B3LYP/6-31G(d):AMBER/ZDO) =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 Mixed
Number of atoms =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I = =A0 =A0 =A0 =A0 =A0 =A0 2048
Charge =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 I =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00
Multiplicity =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02
Number of electrons =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A00
Number of alpha electrons =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A00
Number of beta electrons =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A00
Number of basis functions =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A00
Number of independant functions =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A00
Number of point charges in /Mol/ =A0 =A0 =A0 =A0 =A0 I =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A00
Number of translation vectors =A0 =A0 =A0 =A0 =A0 =A0 =A0I =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A00

How do I get the formatted checkpoint file with the QM-region inside? I
could not find any information nor hints in Gaussian manual.

=A0Thanks, MFX



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