From chemistry-request@server.ccl.net Sun Dec 16 00:10:44 2001 Received: from oxygen.chem.nthu.edu.tw ([140.114.45.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBG5Ahi12870 for ; Sun, 16 Dec 2001 00:10:44 -0500 Received: by oxygen.chem.nthu.edu.tw (Postfix, from userid 212) id 72032154B5; Sun, 16 Dec 2001 13:10:23 +0800 (CST) Date: Sun, 16 Dec 2001 13:10:23 +0800 From: chem@oxygen.chem.nthu.edu.tw To: jmmckel@attglobal.net Cc: chemistry@ccl.net Subject: Re: CCL:F77 to F90/95 Message-ID: <20011216131023.A23841@OXYGEN.chem.nthu.edu.tw> References: <3C1B0E1D.2215B29D@attglobal.net> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <3C1B0E1D.2215B29D@attglobal.net>; from jmmckel@attglobal.net on Sat, Dec 15, 2001 at 08:47:25AM +0000 On Sat, Dec 15, 2001 at 08:47:25AM +0000, jmmckel@attglobal.net wrote: > CCLers, > > On trying the free Intel Linux compiler, largely for F90/F95, on F77 > code the warnings about F77 are quite copious. Is there an F77->F90/95 > utility that will help clear up these warnings? Is there a means to > de-VAXinate F77 code easily? > > Thanks! I'll post the results if there is interest. > For Intel Fortran compiler which supports F90/F95 extensions by default, the following options can be used to keep the backward compability with F77 standard: -cm supress comments for non-standard Fortran, F90/F95 usages -w supress all WAARNING messages (but errors will still be displayed) Sincerely, -- Yu, Jen-Shiang Kenny // jsyu@Platinum.chem.nthu.edu.tw http://oxygen.chem.nthu.edu.tw/~jsyu Theoretical Chemistry Lab, Department of Chemistry, National Tsing Hua University Hsinchu 300, TAIWAN From chemistry-request@server.ccl.net Sun Dec 16 12:45:04 2001 Received: from mta05-svc.ntlworld.com ([62.253.162.45]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBGHj3i30761 for ; Sun, 16 Dec 2001 12:45:03 -0500 Received: from aikiyoga ([80.1.121.10]) by mta05-svc.ntlworld.com (InterMail vM.4.01.03.23 201-229-121-123-20010418) with SMTP id <20011216174444.DTZX27606.mta05-svc.ntlworld.com@aikiyoga>; Sun, 16 Dec 2001 17:44:44 +0000 Message-ID: <005001c18659$1701f4a0$010014ac@aikiyoga> From: "Mire Zloh" To: Subject: Effects of pH - summary Date: Sun, 16 Dec 2001 17:42:53 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_004D_01C18659.16CF9A00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_004D_01C18659.16CF9A00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, thanks to all who answered my question regarding the studies of pH = effects on quantum-chemistry calculations. I am a bit wiser, although there is no strightforward solutions and more = investigations into this problem are necessary.=20 Best regards, Mire From: "Shobe, Dave" Solution studies are still pretty crude at this point (usually just the dielectric constant of the solvent is modeled), and I don't think you = could study the effects of pH using these. One might be able to estimate the = pKa of the molecule, but that's about it. =20 =20 Molecular dynamics is a completely different story, because there you explicitly add solvent molecules (and can have a certain "concentration" = of them protonated or deprotonated). But the sacrifice is that the representation of the molecules are fairly crude, and you will get very little in the way of "electronic properties". =20 =20 If someone actually suggests a way of doing what you want I would be interested in hearing about it. ----- Original Message -----=20 From: "Amiram Goldblum" Maybe I can help a little, but I never used Gamess or MOPAC, while I have much experience with MNDO (which has been part of MOPAC). =20 One way is to study the direct protonation of the molecule, but this = can not be done partially. I am not aware of any such applications, to study continous effects of pH variations on properties, but maybe you could just keep a proton (or oxonium) at varying distances from your molecule in different directions (or maybe a few protons) and recalculate. That would have a differential polarizing effect . In ab initio you will have to take care of the Basis Set Superposition Error (BSSE) - there's quite a lot written about that. The strategy may strongly depend on the structure of your molecules. =20 Many years ago, in the end of the 70's and the during the 80's, Steve Scheiner had a series of papers on the effects of protonation and external charges on molecules. It was really impressive work, done by ab initio mostly. Maybe you should look for them. The average distance of protons is the main effect of pH. You could calculate it from the concentration (probably will be very remote...). From: "Robinson, James" Umm good, errr.. crumbs, I usually add protons or remove them for the appropriate species. AS for a general pH affect, crumbs.. How about = adding H3O+ or OH- in the environment? Or adjust the dielectric constant for = acid or basic media. Cant really think of anything else. ------=_NextPart_000_004D_01C18659.16CF9A00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
thanks to all who answered my question = regarding=20 the studies of pH effects on quantum-chemistry
 calculations.
I am a bit wiser, although there is no=20 strightforward solutions and more investigations into this problem are=20 necessary.
 
Best regards,
 
Mire
 
From: "Shobe, Dave" <dshobe@sud-chemieinc.com>=

Solution studies are still pretty crude at this point (usually just = the
dielectric constant of the solvent is modeled), and I don't think = you=20 could
study the effects of pH using these.  One might be able to = estimate the pKa
of the molecule, but that's about it. =20
 
Molecular dynamics is a completely different story, = because there=20 you
explicitly add solvent molecules (and can have a certain = "concentration"=20 of
them protonated or deprotonated).  But the sacrifice is that=20 the
representation of the molecules are fairly crude, and you will = get=20 very
little in the way of "electronic properties".  =
 
If=20 someone actually suggests a way of doing what you want I would = be
interested=20 in hearing about it.
 
 
----- Original Message -----=20
From: "Amiram Goldblum" <amiram@vms.huji.ac.il>
=
 
Maybe I can help a little, but I never used Gamess or=20 MOPAC,
 while I have much experience with MNDO (which has been = part of=20 MOPAC).
 
One way is to study the direct protonation of the=20 molecule, but this can
 not be done partially. I am not aware of = any=20 such applications,
 to study continous effects of pH variations = on=20 properties,
 but maybe you could just keep  a proton (or=20 oxonium)
 at varying distances from your molecule in=20 different
 directions (or maybe a few protons) and recalculate. = That=20 would have
 a differential polarizing effect . In ab initio you = will=20 have to
 take care of the Basis Set Superposition Error (BSSE) - = there's
 quite a lot written about that. The = strategy
 may=20 strongly depend on the structure of your molecules.
 
Many = years=20 ago, in the end of the 70's and the during the 80's,
 Steve = Scheiner had=20 a series of papers on the effects of protonation
 and external = charges=20 on molecules. It was really impressive work,
 done by ab initio = mostly.=20 Maybe you should look for them.
 The average distance of protons is the main effect of pH. You = could
 calculate it from the concentration (probably will be = very=20 remote...).
 
From: "Robinson, James" <james.robinson@evotecoai.com= >
 
Umm good, = errr.. crumbs,=20 I usually add protons or remove them  for the
 appropriate = species.=20 AS for a general pH affect, crumbs.. How about adding
 H3O+ or = OH- in=20 the environment? Or adjust the dielectric constant for acid
 or = basic=20 media. Cant really think of anything else.
 

------=_NextPart_000_004D_01C18659.16CF9A00-- From chemistry-request@server.ccl.net Sun Dec 16 15:44:20 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fBGKiKU02345 for ; Sun, 16 Dec 2001 15:44:20 -0500 Received: from [165.91.177.236] (account fan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5b3) with ESMTP id 823467 for chemistry@ccl.net; Sun, 16 Dec 2001 14:37:32 -0600 Sender: fan@ccl.net Message-ID: <3C1D0772.1C7B87FB@mail.chem.tamu.edu> Date: Sun, 16 Dec 2001 14:43:30 -0600 From: Hua-Jun Fan Organization: Texas A&M University X-Mailer: Mozilla 4.77C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: symmetry vs standard orietation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netter I seached CCL archieve and found there was a discussion of standard orientation. However, I wasn't able to find the solution to keep G98 from using stardard orientation, yet to still use the symmetry. If I put "NOSYM" in the #-route, then I loose whatever advantages the molecular symmetry gives me in terms of computation time. My question are: 1) does anyone have a way to use the symmetry in the calculation (to save computer time) but stop G98 to re-orientate the molecule during the opt (there is different number of orbital with each irreducible representations when G98 reorientate the molecule) For example, I found in one standard orientation, it shows: ======one orientation==== There are 227 symmetry adapted basis functions of A symmetry. There are 225 symmetry adapted basis functions of B1 symmetry. There are 226 symmetry adapted basis functions of B2 symmetry. There are 226 symmetry adapted basis functions of B3 symmetry. ======another orientation==== There are 227 symmetry adapted basis functions of A symmetry. There are 226 symmetry adapted basis functions of B1 symmetry. There are 226 symmetry adapted basis functions of B2 symmetry. There are 225 symmetry adapted basis functions of B3 symmetry. It seems once G98 use new standard orientation, the B1 and B3 switched. I would like to prevent this happening. 2) does iop(2/15=1) and iop(2/16=3) contradict to each other? Thanks in advance for your time and advice and happy holidays. Huajun