From chemistry-request@ccl.net Mon May 3 22:56:37 2004 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i443uakh007407 for ; Mon, 3 May 2004 22:56:36 -0500 Received: from [172.16.48.146] (account singleton(at)mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro WebUser 4.1.8) with HTTP id 1448287 for CHEMISTRY(at)ccl.net; Mon, 03 May 2004 22:58:20 -0500 From: "Daniel A. Singleton" Subject: CCL:Examples of DG maxima where no PE maximum exists? To: CHEMISTRY(at)ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Mon, 03 May 2004 22:58:20 -0500 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.3 required=7.5 tests=COMBINED_FROM autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net There are a great many such reactions - we have published some, but it is really an old phenomenon. Within physical organic, I would consider Houk's discussion of the addition of carbenes to alkenes in the mid 1980's as a "classic" example. I would guess that a good way to find examples would be to search for "barrierless" reactions, as the scenario you describe will apply to perhaps a majority of reactions described as barrierless. But beware calculationally, entropy at medium intermolecular separations is a four letter word. It is used for some problems, for lack of choice, but buyer beware. On Mon, 3 May 2004 09:19:19 +0100 "Rzepa, Henry" wrote: >In the temporary absence of a working search of the CCL >archives, >does anyone know of any examples of the following >scenario? > >The potential energy surface of a dissociative reaction >may often >rise to the asymptotic maximum of infinite separation of >the two >components. These two components will show a large >increase in >the entropy, and hence any free energy increase for >this process will be >substantially less than the potential energy increase. >Depending >on how the entropy evolves along the reaction path, its >possible to imagine that >unlike the potential energy, the free energy reaction >path may >show a clear maximum (transition state) unmatched by one >in the >potential energy. > >Does anyone know of any "classic" examples of such >entropy induced transition states? >(its the sort of concept that eg a Scifinder search is >difficult >to formulate for) >-- > >Henry Rzepa. Imperial College, Chemistry Dept. >+44 0778 626 8220 +44 020 7594 5804 (Fax) From chemistry-request@ccl.net Tue May 4 06:09:40 2004 Received: from sigfrido.unito.it (sigfrido.unito.it [130.192.119.69]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44B9bkh026756 for ; Tue, 4 May 2004 06:09:38 -0500 Received: (from root@localhost) by sigfrido.unito.it (8.12.antani) id i44BBLS2024628 for chemistry[at]ccl.net; Tue, 4 May 2004 13:11:21 +0200 Received: from ares.unito.it (ares.unito.it [130.192.119.49])by sigfrido.unito.it (8.12.antani) with ESMTP id i44BBLBk024576for ; Tue, 4 May 2004 13:11:21 +0200 Received: from ares (130.192.119.49) by ares.unito.it (7.0.018)id 40927029000169A5 for chemistry[at]ccl.net; Tue, 4 May 2004 13:09:18 +0200 Message-ID: <7815464.1083668958091.JavaMail.root@ares> Date: Tue, 4 May 2004 13:09:18 +0200 (CEST) From: dario longo Reply-To: dario longo To: chemistry[at]ccl.net Subject: problem of Gd-complexes with Gaussian03 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_4502_7338438.1083668958088" X-scanner: scanned by Inflex 1.0.12.7 X-Spam-Status: No, hits=5.0 required=7.5 tests=IMPRONONCABLE_1,J_BACKHAIR_11, J_BACKHAIR_21,J_BACKHAIR_24,J_BACKHAIR_32 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ------=_Part_4502_7338438.1083668958088 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Subject: problem of Gd-complexes with Gaussian03 Dear CCL,I tried to perfor= m geometry optimization of Gd-complexes with ECPof Dolg and Stoll but with = gaussian03 after the first cycle I obtain the follow error: Leave Link 302= at Fri Apr 23 12:56:17 2004, MaxMem=3D 6291456 cpu: 2.3 (Enter /o= pt/gaussian/g03/l303.exe) DipDrv: MaxL=3D1. Leave Link 303 at Fri Apr 23 = 12:56:18 2004, MaxMem=3D 6291456 cpu: 0.1 (Enter /opt/gaussian/g03= /l401.exe) Odd number of core electrons in MinBas. Error termination via Ln= k1e in /opt/gaussian/g03/l401.exe at Fri Apr 23 12:56:18 2004. Job cpu time= : 0 days 0 hours 49 minutes 22.0 seconds. File lengths (MBytes): RWF=3D = 71 Int=3D 0 D2E=3D 0 Chk=3D 14 Scr=3D 1I tried to do= the same calculation with gaussian 98 and it does.In my opinion I think th= at there is a bug in revB.05 of g03 or that I failed to give the right inpu= t file to g03. Can anyone help me?Another question: which is the atomic rad= ii for the Gd in Pop=3DMK?Gaussian 98: SGI-G98RevA.5 Gaussian 03: x86-Lin= ux-G03RevB.05This is the file.com:#P RHF/gen pseudo=3Dread 5d 7f test guess= =3Dcore opt gfpcariche gd_dota rhf geom min -1 1 N 1.643971 -1.25203= 3 -0.976609 N -1.271029 -1.647033 -1.009609 N -1.644029 = 1.251967 -0.977609 N 1.270971 1.646967 -1.009609 O 2.2239= 71 -0.005033 1.425391 O -0.173029 -2.218033 1.446391 O = -2.224029 0.004967 1.425391 O 0.172971 2.217967 1.44639= 1 C 1.068971 -2.631033 -1.607609 C -0.338029 -2.376033 -= 2.157609 C -2.552029 -1.032033 -1.801609 C -2.202029 0.3789= 67 -2.257609 C -1.069029 2.630967 -1.607609 C 0.337971 = 2.375967 -2.157609 C 2.551971 1.031967 -1.801609 C 2.202= 971 -0.378033 -2.257609 C 3.448971 -0.705033 1.007391 C = 3.077971 -1.704033 -0.120609 C -1.050029 -3.357033 1.0903= 91 C -1.933029 -2.955033 -0.113609 C -3.449029 0.704967 = 1.006391 C -3.078029 1.703967 -0.120609 C 1.049971 3.356= 967 1.091391 C 1.932971 2.954967 -0.112609 O 4.583971 = -0.471033 1.405391 O -1.061029 -4.464033 1.612391 O -4.58= 4029 0.470967 1.405391 O 1.060971 4.463967 1.612391 H = 1.762971 -2.949033 -2.393609 H 1.068971 -3.395033 -0.821= 609 H -0.313029 -1.705033 -3.022609 H -0.834029 -3.300033 = -2.470609 H -2.776029 -1.698033 -2.642609 H -3.411029 -1.03= 4033 -1.124609 H -3.067029 0.904967 -2.675609 H -1.415029 = 0.362967 -3.017609 H -1.763029 2.948967 -2.393609 H -1.0= 69029 3.394967 -0.821609 H 0.833971 3.300967 -2.469609 H = 0.313971 1.705967 -3.022609 H 3.410971 1.034967 -1.12= 3609 H 2.775971 1.697967 -2.641609 H 3.066971 -0.905033 = -2.674609 H 1.415971 -0.363033 -3.017609 H 3.881971 -1.7= 69033 -0.858609 H 2.893971 -2.690033 0.320391 H -2.051029 = -3.793033 -0.805609 H -2.913029 -2.638033 0.259391 H -3.= 882029 1.768967 -0.859609 H -2.894029 2.689967 0.320391 H= 2.912971 2.637967 0.259391 H 2.050971 3.792967 -0.8= 05609Gd -0.000029 -0.000033 0.681391 C 03-21g **** N 03-21g ***= * O 03-21g **** H 03-21g ****Gd 0S 3 1.0 7.925043 -0.152264 6.271759 = 0.493923 2.590913 -1.294553S 1 1.0 0.642509 1.0S 1 1.0 0.312826 1.= 0S 1 1.0 0.058480 1.0S 1 1.0 0.026924 1.0P 3 1.0 5.205055 0.114143 = 3.111021 -0.442610 0.743765 1.166532P 1 1.0 0.312702 1.0P 1 1.0 0.09= 4375 1.0P 1 1.0 0.033614 1.0D 3 1.0 2.534209 -0.039487 0.806732 0.39= 0831 0.320355 0.701628D 1 1.00.124207 1.0D 1 1.0 0.048091 1.0 ****GdOP= OT 3 53 D AND UP1 2 1.26200 8.8497760 S-= F2 2 5.02602 139.6016199 2 2.51301 = -6.8796943 P-F2 2 4.3022 79.8738240 2 = 2.15113 0.9384190 D-F2 2 3.0011 32.709729 = 2 1.5055 1.241952Thanks,Dario LongoPhD student Dario LongoDepartme= nt of Chemistry IFMUniversity of Turin, Italydario.longo[at]unito.it _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex ------=_Part_4502_7338438.1083668958088 Content-Type: text/html;charset="UTF-8" Content-Transfer-Encoding: quoted-printable Subject: problem of Gd-complexes with Gaussian03

Dear CCL,
I = tried to perform geometry optimization of Gd-complexes with ECP
of Dolg= and Stoll but with gaussian03 after the first cycle
I obtain the foll= ow error:


Leave Link 302 at Fri Apr 23 12:56:17 2004, MaxMe= m=3D 6291456 cpu: 2.3
(Enter /opt/gaussian/g03/l303.exe)
= DipDrv: MaxL=3D1.
Leave Link 303 at Fri Apr 23 12:56:18 2004, MaxMe= m=3D 6291456 cpu: 0.1
(Enter /opt/gaussian/g03/l401.exe)
= Odd number of core electrons in MinBas.
Error termination via Lnk1e i= n /opt/gaussian/g03/l401.exe at Fri Apr 23 12:56:18 2004.
Job cpu time= : 0 days 0 hours 49 minutes 22.0 seconds.
File lengths (MBytes): RW= F=3D 71 Int=3D 0 D2E=3D 0 Chk=3D 14 Scr=3D 1
I tried to do the same calculation with gaussian 98 and it does.
In m= y opinion I think that there is a bug in revB.05 of g03 or that
I fail= ed to give the right input file to g03. Can anyone help me?
Another que= stion: which is the atomic radii for the Gd in Pop=3DMK?

Gaussian = 98: SGI-G98RevA.5
Gaussian 03: x86-Linux-G03RevB.05

This is= the file.com:

#P RHF/gen pseudo=3Dread 5d 7f test guess=3Dcore op= t gfp

cariche gd_dota rhf geom min

-1 1
N 1.643= 971 -1.252033 -0.976609
N -1.271029 -1.647033 -1.009609=
N -1.644029 1.251967 -0.977609
N 1.270971 1.64= 6967 -1.009609
O 2.223971 -0.005033 1.425391
O -= 0.173029 -2.218033 1.446391
O -2.224029 0.004967 1.4= 25391
O 0.172971 2.217967 1.446391
C 1.068971 = -2.631033 -1.607609
C -0.338029 -2.376033 -2.157609
C= -2.552029 -1.032033 -1.801609
C -2.202029 0.378967 = -2.257609
C -1.069029 2.630967 -1.607609
C 0.33797= 1 2.375967 -2.157609
C 2.551971 1.031967 -1.801609 C 2.202971 -0.378033 -2.257609
C 3.448971 -0.7050= 33 1.007391
C 3.077971 -1.704033 -0.120609
C -1.= 050029 -3.357033 1.090391
C -1.933029 -2.955033 -0.113= 609
C -3.449029 0.704967 1.006391
C -3.078029 1= .703967 -0.120609
C 1.049971 3.356967 1.091391
C = 1.932971 2.954967 -0.112609
O 4.583971 -0.471033 = 1.405391
O -1.061029 -4.464033 1.612391
O -4.584029 = 0.470967 1.405391
O 1.060971 4.463967 1.612391
H 1.762971 -2.949033 -2.393609
H 1.068971 -3.395033= -0.821609
H -0.313029 -1.705033 -3.022609
H -0.83= 4029 -3.300033 -2.470609
H -2.776029 -1.698033 -2.64260= 9
H -3.411029 -1.034033 -1.124609
H -3.067029 0.9= 04967 -2.675609
H -1.415029 0.362967 -3.017609
H = -1.763029 2.948967 -2.393609
H -1.069029 3.394967 -0.= 821609
H 0.833971 3.300967 -2.469609
H 0.313971 = 1.705967 -3.022609
H 3.410971 1.034967 -1.123609
= H 2.775971 1.697967 -2.641609
H 3.066971 -0.905033 = -2.674609
H 1.415971 -0.363033 -3.017609
H 3.8819= 71 -1.769033 -0.858609
H 2.893971 -2.690033 0.320391<= br/> H -2.051029 -3.793033 -0.805609
H -2.913029 -2.638= 033 0.259391
H -3.882029 1.768967 -0.859609
H -2= .894029 2.689967 0.320391
H 2.912971 2.637967 0.25= 9391
H 2.050971 3.792967 -0.805609
Gd -0.000029 -= 0.000033 0.681391

C 0
3-21g
****
N 0
3-21= g
****
O 0
3-21g
****
H 0
3-21g
****
Gd 0
S 3 1.0
7.925043 -0.152264
6.271759 0.493923
= 2.590913 -1.294553
S 1 1.0
0.642509 1.0
S 1 1.0
0.3= 12826 1.0
S 1 1.0
0.058480 1.0
S 1 1.0
0.026924 1= .0
P 3 1.0
5.205055 0.114143
3.111021 -0.442610
0.7= 43765 1.166532
P 1 1.0
0.312702 1.0
P 1 1.0
0.094375 = 1.0
P 1 1.0
0.033614 1.0
D 3 1.0
2.534209 -0.039487<= br/> 0.806732 0.390831
0.320355 0.701628
D 1 1.0
0.124207 = 1.0
D 1 1.0
0.048091 1.0
****

Gd
OPOT 3 53 D AND UP
1
2 1.26200 8.8497760
= S-F
2
2 5.02602 139.6016199
= 2 2.51301 -6.8796943
P-F
2
2 = 4.3022 79.8738240
2 2.15113 0.9384190
= D-F
2
2 3.0011 32.709729
2 1.5= 055 1.241952

Thanks,
Dario Longo


PhD student= Dario Longo
Department of Chemistry IFM
University of Turin, Italy=

dario.longo[at]unito.it
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Tue, 4 May 2004 04:59:49 -0500 Received: from araneus.saclay.cea.fr (araneus.saclay.cea.fr [132.166.192.110]) by sainfoin.extra.cea.fr (8.12.10/CEAnet-Internet.3.0) with ESMTP id i44A1Vbe020512 for ; Tue, 4 May 2004 12:01:31 +0200 (MEST) Received: from nenuphar.saclay.cea.fr (unverified) by araneus.saclay.cea.fr (Content Technologies SMTPRS 4.3.12) with ESMTP id ; Tue, 4 May 2004 12:01:31 +0200 Received: from llb.saclay.cea.fr (llb.saclay.cea.fr [132.166.17.100]) by nenuphar.saclay.cea.fr (8.12.10/CEAnet-Internes.3.0) with ESMTP id i44A1VSw002079; Tue, 4 May 2004 12:01:31 +0200 (MEST) Received: from [132.166.18.220] (llb1220.saclay.cea.fr [132.166.18.220]) by llb.saclay.cea.fr (8.12.10/jtpda-5.3.2) with ESMTP id i44A1S7o001422 ; Tue, 4 May 2004 12:01:29 +0200 (MEST) In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v613) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Message-Id: <080F78D8-9DB2-11D8-B1F4-000A95999556/at/cnrs-orleans.fr> Cc: From: Konrad Hinsen Subject: Re: CCL:Rigid body simulations in charmm Date: Tue, 4 May 2004 12:01:37 +0200 To: Ravindra VenKatramani X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i449xokh023456 On May 3, 2004, at 7:02, Ravindra VenKatramani wrote: > My first thought is to define the dipeptide structure only > thorugh > bonds (no angles or dihederals) and use SHAKE to keep the peptide > fixed. > Doing so i`m running into SHAKE convergence problems during the heating > and equilibration stage. Am i missing something in this simple minded > approach? Is there an alternate way to perform rigid body simulations? > Standard SHAKE is not suited for rigid bodies exceeding four atoms. There is an extension for those cases, but it doesn't seem to be very popular. There are also many other algorithms for simulating rigid molecules. However, I don't know if any of them are available in CHARMM. -- --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lion Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen/at/llb.saclay.cea.fr --------------------------------------------------------------------- From chemistry-request@ccl.net Tue May 4 04:02:14 2004 Received: from relay.uva.es (relay.uva.es [157.88.18.241]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4492Ckh020597 for ; Tue, 4 May 2004 04:02:13 -0500 Received: from relay.uva.es (localhost [127.0.0.1]) by relay.uva.es (8.12.10/8.12.10) with ESMTP id i4493tPp030024 for ; Tue, 4 May 2004 11:03:56 +0200 Received: from Debug (iscar.cpd.uva.es [157.88.18.32]) by relay.uva.es (8.12.10/8.12.10) with SMTP id i4493ttv030019 for ; Tue, 4 May 2004 11:03:55 +0200 Message-Id: <200405040903.i4493ttv030019^at^relay.uva.es> To: chemistry^at^ccl.net From: Marma Eugenia Sanz Subject: VibRot calculation problem with Gaussian Date: Tue, 4 May 2004 11:03:57 MET X-Posting-IP: 157.88.37.148 X-Mailer: Endymion MailMan Professional Edition v3.2.9 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi to all, I had a problem when I tried to calculate vibration-rotation coupling in a linear molecule using Gaussian, and I wonder if somebody can give me any advice on it. The calculations were run at the MP2 level of theory, with the following line in the route section for the job: #MP2/6-311++G(d,p) Opt=Z-matrix density=current Freq=(VibRot) The job run perfectly until it got to the Freq calculation part. It calculated the harmonic frequencies and the zero-point correction, but it stopped when it began the vibro-rotational analysis saying that an arithmetic exception occurred. Any help will be greatly appreciated. Sincerely, Marma E. Sanz Departamento de Qummica Fmsica y Qummica Inorganica Universidad de Valladolid Prado de la Magdalena, s/n 47005 Valladolid (Spain) Email: mesanz^at^qf.uva.es From chemistry-request@ccl.net Tue May 4 10:18:55 2004 Received: from postoffice9.mail.cornell.edu (postoffice9.mail.cornell.edu [132.236.56.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44FIskh006206 for ; Tue, 4 May 2004 10:18:54 -0500 Received: from cornell.edu ([128.84.183.113]) by postoffice9.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i44FKd6h008249 for ; Tue, 4 May 2004 11:20:40 -0400 (EDT) Date: Tue, 4 May 2004 11:20:40 -0400 Subject: Re: CCL:Rigid body simulations in charmm Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v553) From: Richard Gillilan To: chemistry)at(ccl.net Content-Transfer-Encoding: 7bit In-Reply-To: <1D3622FF-9D3B-11D8-BAEC-000393D59F68)at(cornell.edu> Message-Id: <9A91BB00-9DDE-11D8-BAEC-000393D59F68)at(cornell.edu> X-Mailer: Apple Mail (2.553) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > codes are available anywhere yet. The older program DPOLY > can do this kind of simulation. Sorry for my poor choice of words here (the program is actively maintained and fairly recent) and the typo, the program is called DL_POLY and can be found at http://www.cse.clrc.ac.uk/msi/software/DL_POLY/. Looks like it has been used for liquid simulations too. Richard Gillilan MacCHESS, Cornell From chemistry-request@ccl.net Tue May 4 11:08:10 2004 Received: from mail.scs.uiuc.edu (mail.scs.uiuc.edu [130.126.231.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44G89kh008821 for ; Tue, 4 May 2004 11:08:10 -0500 Received: from leonidas (leonidas.scs.uiuc.edu [130.126.226.239]) by mail.scs.uiuc.edu with esmtp; Tue, 04 May 2004 11:09:52 -0500 Reply-To: jerome~at~scs.uiuc.edu From: "Jerome Baudry" To: "'Ravindra VenKatramani'" Cc: chemistry~at~ccl.net Subject: RE: Rigid body simulations in charmm Date: Tue, 4 May 2004 11:07:33 -0500 Message-ID: <004401c431f1$e9339e10$efe27e82@leonidas> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 In-Reply-To: <080F78D8-9DB2-11D8-B1F4-000A95999556~at~cnrs-orleans.fr> Importance: Normal X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net What about fixing all internal coordinates in the to-be-rigid-molecule: using the CONS ICcommand ? all bonds must have the same restraint constant (same for angles, dihedrals etc..) , but since you want to define a rigid body, you can use one unique very high constant. You would have to define explicitly all ICs in the CONS IC command, but doable since you're dealing with a dipeptide.. ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome~at~scs.uiuc.edu > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request~at~ccl.net]On > Behalf Of Konrad Hinsen > Sent: Tuesday, May 04, 2004 5:02 AM > To: Ravindra VenKatramani > Cc: chemistry~at~ccl.net > Subject: CCL:Rigid body simulations in charmm > > > On May 3, 2004, at 7:02, Ravindra VenKatramani wrote: > > > My first thought is to define the dipeptide structure only > > thorugh > > bonds (no angles or dihederals) and use SHAKE to keep the peptide > > fixed. > > Doing so i`m running into SHAKE convergence problems during > the heating > > and equilibration stage. Am i missing something in this > simple minded > > approach? Is there an alternate way to perform rigid body > simulations? > >> From chemistry-request@ccl.net Tue May 4 11:58:24 2004 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44GwNkh011608 for ; Tue, 4 May 2004 11:58:23 -0500 Received: from localhost (localhost [127.0.0.1]) by pickering.cc.nd.edu (Switch-3.1.4/Switch-3.1.0) with ESMTP id i44H087u021119 for ; Tue, 4 May 2004 12:00:08 -0500 (EST) Received: from laptop.ccl.net (laptop.ccl.net [129.74.52.62]) by webmail.nd.edu (IMP) with HTTP for ; Tue, 4 May 2004 12:00:08 -0500 Message-ID: <1083690008.4097cc1894f98|at|webmail.nd.edu> Date: Tue, 4 May 2004 12:00:08 -0500 From: Jan K Labanowski To: chemistry|at|ccl.net Subject: 04.09.16 Workshop "Modelling & Design of Molecular Materials, Wroclaw, Poland MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 129.74.52.62 X-ND-MTA-Date: Tue, 04 May 2004 12:00:09 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4357 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Date: Sun, 25 Apr 2004 20:55:41 +0200 (CEST) From: Andrzej Sokalski Reply-To: Andrzej Sokalski Subject: Workshop "Modelling & Design of Molecular Materials To: jkl|at|ccl.net Workshop Modelling & Design of Molecular Materials in Wroclaw, Poland - September 16-20, 2004 ORGANIZERS: Molecular Modelling Laboratory, Wroclaw University of Technology NSF Computational Center for Molecular Structure & Interactions Jackson State University, Jackso, MS, USA Charles University in Prague, Czech Republic Polish Chemical Society TOPICS: Workshop will be devoted to presentation of the contemporary computational methods and their applications in molecular modeling and design of molecular materials. Part of the lectures will be given by experimentalists involved in synthesis and testing of novel designed materials. PLANNED SESSIONS: modelling biopolymer structure modelling chemical reactions modelling molecular materials design and synthesis of molecular materials software presentations poster session WWW PAGE: http://mml.ch.pwr.wroc.pl/workshop/ CONTACT ADDRESS: Prof. W. Andrzej Sokalski Institute of Physical and Theoretical Chemistry I-30 Chemistry Department, Wroclaw University of Technology Wybrzeze Wyspianskiego 27 50-370 Wroclaw, Poland tel: +48 (71) 320 2457 fax: +48 (71) 320 3364 sokalski|at|pwr.wroc.pl or workshop|at|mml.ch.pwr.wroc.pl From chemistry-request@ccl.net Tue May 4 11:16:51 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44GGhkh009122 for ; Tue, 4 May 2004 11:16:50 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id BF78F47F1F; Tue, 4 May 2004 12:17:35 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 01933-08; Tue, 4 May 2004 12:17:35 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com (srvkyem1.americas.sc-world.com [10.16.100.68]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 7F390490B8; Tue, 4 May 2004 12:14:27 -0400 (EDT) content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C431F2.DF617B9A" X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 Subject: RE: [Q] SP with CBS-QB3 is possible? Date: Tue, 4 May 2004 12:14:27 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FD4B{at}srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: [Q] SP with CBS-QB3 is possible? Thread-Index: AcQx64GEDYcdx/w+RwecF0qjLLJuigABeGzg From: "Shobe, David" To: "Hohjai Lee" , X-Spam-Status: No, hits=5.2 required=7.5 tests=HTML_20_30,HTML_FONTCOLOR_BLUE, HTML_FONTCOLOR_UNKNOWN,HTML_MESSAGE,MY_HTML_OBFU,NO_RDNS2,WEIRD_PORT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C431F2.DF617B9A Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable I asked Gaussian Inc. this question some years ago (which means that = G98W was the program in question) and they gave me this IOP command: = iop(1/7=3D1000000). What this really does is set the force and = displacement tolerances so loose that every halfway-reasonable geometry = is considered to be "optimized". The program will still go through the = motions of geometry optimization and frequency calculation, but the = geometry will still be the one you input. =20 =20 If you use this iop command, YOU MUST IGNORE anything generated by the = freq calculation step! Vibrational frequencies, intensities, = thermochemistry will all be incorrect!! This is a "side effect" of = using this iop command. =20 --David Shobe, Ph.D., M.L.S.=20 Sud-Chemie, Inc.=20 phone (502) 634-7409=20 fax (502) 634-7724=20 Don't bother flaming me: I'm behind a firewall.=20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request{at}ccl.net]On = Behalf Of Hohjai Lee Sent: Tuesday, May 04, 2004 9:43 AM To: chemistry{at}ccl.net Subject: CCL:[Q] SP with CBS-QB3 is possible? Dear colleague,=20 According to the Gaussian98 manual, SP (single point) keyword can be = applied to ALL method including complete basis set methods.=20 Now I'm trying to get a single point energy by the CBS-QB3, and write = the route line as=20 #T CBS-QB3 SP=20 However, it found that it initaily geometry optimization process.=20 Isn't it possible to carry out single point energy calculation by = CBS-QB3?=20 Thank you!=20 Hohjai Lee (hohjai_y{at}korea.ac.kr)=20 -------------------------------------------------------------------------= ----- Hohjai Lee=20 Nano&Environmental Science Lab. 503, Asan Science Hall, Dep't of Chemistry, Korea Univ. 5-1, Anam-dong, Sungbuk-gu, Seoul, 136-701 KOREA=20 Tel : (+82)-2-3290-3617, (+82)-2-3290-3550 FAX : (+82)-2-3290-3121=20 E-mail : hohjai_y{at}korea.ac.kr=20 Homepage : http://neslab.korea.ac.kr = =20 ------_=_NextPart_001_01C431F2.DF617B9A Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable
I=20 asked Gaussian Inc. this question some years ago (which means that G98W = was the=20 program in question) and they gave me this IOP command: iop(1/7=3D1000000).  What this really = does is set the=20 force and displacement tolerances so loose that every halfway-reasonable = geometry is considered to be "optimized".  The program will still = go=20 through the motions of geometry optimization and frequency calculation, = but the=20 geometry will still be the one you input.  =
 
If you=20 use this iop command, YOU MUST IGNORE anything generated by the freq = calculation=20 step!  Vibrational frequencies, intensities, thermochemistry will = all be=20 incorrect!!  This is a "side effect" of using this iop=20 command.
 

--David Shobe, Ph.D., M.L.S. =
Süd-Chemie, Inc.
phone=20 (502) 634-7409
fax (502) = 634-7724

Don't bother flaming me: I'm behind a=20 firewall.

-----Original Message-----
From: Computational = Chemistry List=20 [mailto:chemistry-request{at}ccl.net]On Behalf Of Hohjai=20 Lee
Sent: Tuesday, May 04, 2004 9:43 AM
To:=20 chemistry{at}ccl.net
Subject: CCL:[Q] SP with CBS-QB3 is=20 possible?

Dear colleague,

According to the = Gaussian98 manual, SP (single point) keyword can be applied to ALL = method=20 including complete basis set methods.
Now I'm trying to get a = single point=20 energy by the CBS-QB3, and write the route line as

#T CBS-QB3 = SP=20

However, it found that it initaily geometry optimization = process.=20
Isn't it possible to carry out single point energy calculation by = CBS-QB3?=20

Thank you!

Hohjai Lee (hohjai_y{at}korea.ac.kr)

-------------------------------------------------------= -----------------------

Hohjai Lee

Nano&Environmental Science Lab.

503, Asan Science Hall, Dep't of Chemistry, Korea=20 Univ.

5-1, Anam-dong, Sungbuk-gu, Seoul, 136-701 KOREA =

Tel : (+82)-2-3290-3617, (+82)-2-3290-3550 FAX :=20 (+82)-2-3290-3121

E-mail : hohjai_y{at}korea.ac.kr

Homepage : http://neslab.korea.ac.kr

------_=_NextPart_001_01C431F2.DF617B9A-- From chemistry-request@ccl.net Tue May 4 13:55:47 2004 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44Ithkh021405 for ; Tue, 4 May 2004 13:55:44 -0500 Received: from yakko (localhost [127.0.0.1]) by localhost.cimav.edu.mx (Postfix) with ESMTP id E9A1A1B8012; Tue, 4 May 2004 12:57:21 -0600 (MDT) Received: from localhost ([127.0.0.1]) by yakko.cimav.edu.mx (MailMonitor for SMTP v1.2.2 ) ; Tue, 4 May 2004 12:57:21 -0600 (MDT) Received: from laquicom05 (byron.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (Postfix) with ESMTP id 4C6E71B801A; Tue, 4 May 2004 12:57:16 -0600 (MDT) From: "Dr. Daniel Glossman-Mitnik" To: , Subject: CCL: questions about G03W functionalities Date: Tue, 4 May 2004 12:57:23 -0600 Message-ID: <000301c43209$a2d52a70$df01000a@laquicom05> MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_NextPart_000_0004_01C431D7.583F4E50" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.6626 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=2.5 required=7.5 tests=COMBINED_FROM,HTML_70_80, HTML_FONTCOLOR_BLUE,HTML_FONTCOLOR_UNKNOWN,HTML_FONT_BIG,HTML_MESSAGE, NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0004_01C431D7.583F4E50 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0005_01C431D7.5843E230" ------=_NextPart_001_0005_01C431D7.5843E230 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 =20 =20 Dear netters !!! =20 I have several questions regarding the functionalities in G03W: =20 1) The implementation of ONIOM within G03W allows the calculation of atomic charges according to some population analysis ?=20 The results given by GaussViewW are those charges or it is=20 necessary to do some additional algebraic operations ? =20 2) Is it possible to calculate polarizabilities with ONIOM in G03W ? How are they obtained ? =20 3) According to the Gaussian brochure, it should be possible to calculate NMR shifts within ONIOM, but GaussViewW does not have this option ? How this can be circunvected ? =20 4) In the literature, a ONIOM-PCM has been described. Has it been Implemented in G03W ? =20 5) What about calculating UV spectra with ONIOM ? =20 6) In G03W there is an option for doing PBC calculations. Where can I find information (and examples) on how to construct the = input for that kind of calculations ? (i.e., how do you know the translation vectors? ) =20 Thanks in advance. =20 Best regards =20 Dr. Daniel Glossman-Mitnik=20 =20 *************************************************************************= *** ****************** Dr. Daniel Glossman-Mitnik =20 CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC=20 QCyNAM - Grupo de Qu=EDmica Computacional y Nanotecnolog=EDa Molecular Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel=E9fono: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman.-at-.cimav.edu.mx dglossman.-at-.prodigy.net.mx *************************************************************************= *** *******************=20 =20 ------=_NextPart_001_0005_01C431D7.5843E230 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

 

 

 

Dear netters !!!

 

I have several = questions regarding the functionalities in G03W:

 

1)=    The implementation of ONIOM within = G03W allows the calculation

  &nbs= p;  of atomic charges according to some population analysis ? =

  &nbs= p;  The results given by GaussViewW are those charges or it is =

  &nbs= p;  necessary to do some additional algebraic operations ?

 

2)   Is it possible to calculate polarizabilities = with ONIOM in G03W ?

  &nbs= p;        How are they obtained ?

 

3)   According to the Gaussian brochure, it should = be possible to

  &nbs= p;  calculate  NMR shifts within ONIOM, but GaussViewW does = not

  &nbs= p;   have this option ? How this can be circunvected ?

 

4)   In the literature, a ONIOM-PCM has been = described. Has it been

  &nbs= p;  Implemented in G03W ?

 

5)   What about calculating UV spectra with ONIOM = ?

 

6)   In G03W  there is an option for doing PBC calculations. Where can

  &nbs= p;        I find information (and examples) on how to construct the input = for

  &nbs= p;        that kind of calculations ? (i.e., how do you know the = translation

  &nbs= p;        vectors? )

 

Thanks in = advance.

 

Best = regards

 

  &nbs= p;            = ;            =             Dr. Daniel Glossman-Mitnik

 

****************= *************************************************************************= *****

  &nbs= p;          = Dr. Daniel Glossman-Mitnik

 

CIMAV - Centro de Investigaci=F3n = en Materiales Avanzados, SC

QCyNAM - Grupo de Qu=EDmica Computacional y Nanotecnolog=EDa = Molecular

Miguel de Cervantes 120 - Complejo Industrial Chihuahua

Chihuahua, Chih. 31109 - = MEXICO

Tel=E9fono: (52) 614 4391151           =      FAX:       (52) 614 = 4391112

      = ;        dglossman.-at-.prodigy.net.mx

***********************************= ************************************************************ 

 <= /font>

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charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Subject: Data pipelining seminars in US and Canada Date: Tue, 4 May 2004 12:23:23 -0700 Message-ID: <830D8D4719112B418ABBC3A0EBA95812545B15|at|webmail.scitegic.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Data pipelining seminars in US and Canada Thread-Index: AcQx60MmVbKNWgqKTCiSKkXrFpR9MA== From: "Rob Brown" To: , X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i44JLckh022236 Dear Colleagues SciTegic will be hosting a series of free lunch seminars in the US and Canada in May and June. "Data Pipelining - A Novel Approach to Scientific Data and Application Integration" The morning session will discuss will discuss challenges and solutions for the integration, organization and reporting of discovery data. The afternoon session will cover informatics solutions for building and deploying a virtual high throughput screening system. Guest speakers will include: Frank Brown, Senior Research Fellow, Johnson & Johnson Research & Development, L.L.C Giles Day, Director, Site Head Research Informatics, Research Technology Center, Pfizer Global R&D Scott D. Bembenek, Scientist, Computer Aided Drug Design, Johnson & Johnson Pharmaceutical Research & Development Michael Hack, Scientist, Computer Aided Drug Design, Johnson & Johnson Pharmaceutical Research & Development Jennifer Kelly Shepphird, Application Scientist, Tripos, Inc. Paul Hawkins, Application Scientist, Tripos, Inc. Dates and locations are as follows: May 24, San Diego, CA at Ruth's Chris May 25, San Mateo, CA at 231 Ellsworth May 26, Vancouver, BC at Four Seasons June 8, Durham, NC at Cafi Parizade June 9, Princeton, NJ at Le Plumet Royal at the Peacock Inn June 10, New Haven, CT at Zinc June 11, Montreal, QC at Les Chevres For details of the agenda and how to register please visit http://www.scitegic.com/seminars Regards, Rob Brown SciTegic Inc From chemistry-request@ccl.net Tue May 4 14:13:53 2004 Received: from mail.pas.rochester.edu (mail1.pas.rochester.edu [128.151.144.211]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44JDqkh021790 for ; Tue, 4 May 2004 14:13:52 -0500 Received: from localhost.localdomain (localhost.localdomain [127.0.0.1]) by mail.pas.rochester.edu (Postfix) with ESMTP id C26CA1E15E6; Tue, 4 May 2004 15:15:34 -0400 (EDT) Received: from mail.pas.rochester.edu (localhost.localdomain [127.0.0.1]) by localhost.localdomain (VaMailArmor-2.0.1.13) id 03348-3C5C769E; Tue, 04 May 2004 15:15:34 -0400 Received: from nowshell.pas.rochester.edu (nowshell.pas.rochester.edu [128.151.144.230]) by mail.pas.rochester.edu (Postfix) with ESMTP id B1DBB1E159A; Tue, 4 May 2004 15:15:34 -0400 (EDT) Date: Tue, 4 May 2004 15:15:37 -0400 (EDT) From: Ravindra VenKatramani To: Jerome Baudry Cc: Subject: RE: Rigid body simulations in charmm In-Reply-To: <004401c431f1$e9339e10$efe27e82@leonidas> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-AntiVirus: checked by Vexira MailArmor (version: 2.0.1.13; VAE: 6.25.0.3; VDF: 6.25.0.47; host: mail1.pas.rochester.edu) X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Yes, This was also suggested by Rick Venable in response to my mail and i think it`s the best way to proceed. I now define all the bonds for my dipeptide and then use IC GENERATE, IC FILL (I have the cartesian coords) and CONS IC BONDS ANGLES DIHED IMPR to hold the peptide fixed. It seems that i do not need to specify the IC`s by hand as charmm can generate them from the bond information. One question is what is the upper limit on the force constant values? it should depend on the timestep right? Regards Ravi On Tue, 4 May 2004, Jerome Baudry wrote: > What about fixing all internal coordinates in the to-be-rigid-molecule: > using the CONS ICcommand ? > all bonds must have the same restraint constant (same for angles, dihedrals > etc..) , but since you want to define a rigid body, you can use one unique > very high constant. You would have to define explicitly all ICs in the CONS > IC command, but doable since you're dealing with a dipeptide.. > > > ---------------------------------------------------------- > Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. > School of Chemical Sciences University of Illinois at Urbana-Champaign > 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 > Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: > jerome|at|scs.uiuc.edu > > > > -----Original Message----- > > From: Computational Chemistry List > > [mailto:chemistry-request|at|ccl.net]On > > Behalf Of Konrad Hinsen > > Sent: Tuesday, May 04, 2004 5:02 AM > > To: Ravindra VenKatramani > > Cc: chemistry|at|ccl.net > > Subject: CCL:Rigid body simulations in charmm > > > > > > On May 3, 2004, at 7:02, Ravindra VenKatramani wrote: > > > > > My first thought is to define the dipeptide structure only > > > thorugh > > > bonds (no angles or dihederals) and use SHAKE to keep the peptide > > > fixed. > > > Doing so i`m running into SHAKE convergence problems during > > the heating > > > and equilibration stage. Am i missing something in this > > simple minded > > > approach? Is there an alternate way to perform rigid body > > simulations? > > >> > > From chemistry-request@ccl.net Tue May 4 14:13:57 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44JDtkh021794 for ; Tue, 4 May 2004 14:13:56 -0500 Received: from frenkel.ps.uci.edu (frenkel.ps.uci.edu [128.200.11.119]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id i44JFSI4026178 for ; Tue, 4 May 2004 12:15:32 -0700 Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz:at:mail.rochester.edu Organization: university of california at Irvine To: chemistry:at:ccl.net Subject: install charmm C27b1 in linux cluster with SUSE system Date: Tue, 4 May 2004 12:16:23 -0400 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200405041216.23560.wzhuang:at:uci.edu> X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=2.9 required=7.5 tests=IMPRONONCABLE_1, IMPRONONCABLE_2,UPPERCASE_25_50 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i44JDvkh021818 Hi, all: when I try to install charmm C27b1 in my linux cluster, I type in: ******************* install gnu large g77 *********************** and the compilation doesn't give out the executable,and in the gnu.log, it said: *************************** CHARMM Build on gnu Tue May 4 11:59:45 PDT 2004 /usr/local/charmmfresh/c27b1/tool/preflx /usr/local/charmmfresh/c27b1/source/adumb/cmds.src 53 Conditional keys: GNU UNIX SCALAR CMPI MPI PARALLEL GENCOMM PARAFULL LARGE PUTFCM OLDDYN PBOUND Conditional keys: ACE ADUMB ASPENER BLOCK CFF DIMB DMCONS DOCK FOURD FMA GENETIC GENBORN Conditional keys: GBINLINE GBSWIT IMCUBES LATTICE LDM LONEPAIR MC MMFF MOLVIB MTS MULTCAN PATHINT Conditional keys: PBEQ PERT PM1 PNOE POLAR PRIMSH REPLICA RGYCONS RISM RXNCOR SHAPES SOFTVDW Conditional keys: TNPACK TRAVEL TSM QUANTUM NOGRAPHICS g77 -malign-double -fno-f2c -fno-backslash -O2 -fugly-complex -fno-globals -Wno-globals -DGNU -c cmds.f f771: error: -malign-double makes no sense in the 64bit mode make: *** [/usr/local/charmmfresh/c27b1/lib/gnu/adumb.a(cmds.o)] Error 1 ******************************************** can anyone tell me what is going on? wei zhuang From chemistry-request@ccl.net Tue May 4 16:46:26 2004 Received: from postfix4-1.free.fr (postfix4-1.free.fr [213.228.0.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i44LkNkh026853 for ; Tue, 4 May 2004 16:46:23 -0500 Received: from [82.65.140.33] (lns-p19-19-82-65-140-33.adsl.proxad.net [82.65.140.33]) by postfix4-1.free.fr (Postfix) with ESMTP id 8896D105F54; Tue, 4 May 2004 23:48:07 +0200 (CEST) In-Reply-To: <004401c431f1$e9339e10$efe27e82@leonidas> References: <004401c431f1$e9339e10$efe27e82@leonidas> Mime-Version: 1.0 (Apple Message framework v613) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <0E302AF6-9E15-11D8-BC51-000A95AB5F10{at}cnrs-orleans.fr> Content-Transfer-Encoding: 7bit Cc: "'Ravindra VenKatramani'" , chemistry{at}ccl.net From: hinsen{at}cnrs-orleans.fr Subject: Re: CCL:Rigid body simulations in charmm Date: Tue, 4 May 2004 23:50:27 +0200 To: "Jerome Baudry" X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=4.0 required=7.5 tests=MY_DSL,NO_REAL_NAME, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 04.05.2004, at 18:07, Jerome Baudry wrote: > What about fixing all internal coordinates in the to-be-rigid-molecule: > using the CONS ICcommand ? > all bonds must have the same restraint constant (same for angles, > dihedrals > etc..) , but since you want to define a rigid body, you can use one > unique > very high constant. You would have to define explicitly all ICs in the > CONS > IC command, but doable since you're dealing with a dipeptide.. If I understand correctly what this command does, it adds a restraint force. This is *not* equivalent to fixing a coordinate. There is an important technical difference (a high force constant requires a very short integration time step, whereas a fixed internal coordinate permits a larger one), and also a difference in thermodynamic averages. The limit of a restraint force when the force constant goes to infinity is not a fixed coordinate. Depending on the application, this point may not be important, but one should be aware of it. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen{at}llb.saclay.cea.fr ------------------------------------------------------------------------ -------