From owner-chemistry@ccl.net Thu Apr 20 05:53:00 2006 From: "Eduard Matito ematito.(~).gmail.com" To: CCL Subject: CCL: AIM charges - HF or DFT? Message-Id: <-31561-060419195517-13538-HGgAvPI5ITmk0fZk+geSvQ(~)server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 20 Apr 2006 00:56:07 +0200 MIME-Version: 1.0 Sent to CCL by: Eduard Matito [ematito .. gmail.com] Dear Mark, Sorry, because certainly my answer could lead to confusion. What I meant is that, since the HF wavefunction is the monodeterminantal wavefunction that minimizes the electron energy of the true Hamiltonian, one would anticipate it as the monodeterminantal one that better approches variationally the problem. On the other hand, the "Kohn-Sham wavefunction" minimizes the energy of a different Hamiltonian, and thus it is difficult to know what comes out of it. I would agree that maybe the KS orbitals would lead to a better density as compared to the true one. But actually I do not expect them to produce better wave function, or better pair density than the HF one. Eduard Mark Zottola mzottola:_:gmail.com wrote: >Sent to CCL by: "Mark Zottola" [mzottola{=}gmail.com] >------=_Part_73906_5855828.1145460402501 >Content-Type: text/plain; charset=ISO-8859-1 >Content-Transfer-Encoding: quoted-printable >Content-Disposition: inline > >I have never heard this statement (see below) proffered nor defended. Are >there references to substantiate this statement?? More over, it is truly >difficult to believe that an RHF wavefunction provides a better wavefunctio= >n >than say B3LYP (at an identical basis set) for the description of electron >density topology. Are there references to substantiate such an unusual >claim? > > >Mark > > Eduard Matito Institute of Computational Chemistry University of Girona (Spain) e-mail: eduard(at)iqc.udg.es http://iqc.udg.es/~eduard From owner-chemistry@ccl.net Thu Apr 20 06:28:00 2006 From: "Gerhard Goldbeck-Wood gerhard-$-accelrys.com" To: CCL Subject: CCL: Imidazoliums Message-Id: <-31562-060420054243-16690-QoPz11MhY3au1fz3RonPoA!A!server.ccl.net> X-Original-From: Gerhard Goldbeck-Wood Content-Type: multipart/alternative; boundary="=_alternative 0030CCE580257156_=" Date: Thu, 20 Apr 2006 09:53:21 +0100 MIME-Version: 1.0 Sent to CCL by: Gerhard Goldbeck-Wood [gerhard^accelrys.com] This is a multipart message in MIME format. --=_alternative 0030CCE580257156_= Content-Type: text/plain; charset="US-ASCII" There is a new review article on the subject matter which may be of interest: Molecular Simulation Publisher: Taylor & Francis Issue: Volume 32, Number 01 / January 2006 Pages: 1 - 10 DOI: 10.1080/08927020500486627 The simulation of imidazolium-based ionic liquids P. A. Hunt Imperial College London, Chemistry Department, London, SW7 2AZ, UK Gerhard Goldbeck-Wood, PhD Nanotechnology Consortium Director Accelrys "Chris Moth chris.moth*o*vanderbilt.edu" Sent by: owner-chemistry+/-ccl.net 20/04/2006 02:37 Please respond to "CCL Subscribers" To "Goldbeck-Wood, Gerhard " cc Subject CCL: Imidazoliums Sent to CCL by: Chris Moth [chris.moth^^vanderbilt.edu] You might take a peek at the "HIP" (protonated histidine) residue in the AMBER force field for some inspiration/validation. See page 5190 of Cornell et. al, J. Am. Chem. SOC. 1995, 117, 5179-5197 Though, imidazolium should likely be parameterized in the context of your particular MD force field. John Daily john.daily],[colorado.edu wrote: > Sent to CCL by: John Daily [john.daily,colorado.edu] > > --Apple-Mail-3--396696999 > Content-Transfer-Encoding: 7bit > Content-Type: text/plain; > charset=US-ASCII; > delsp=yes; > format=flowed > > Folks, > > Does anyone have experience with charged imidazoliums? I am doing > molecular dynamic calculations on small droplets of ionic liquids. > Obviously as the size of the drops increases, using quantum methods > gets too expensive. However, I have not been able to find force field > parameters for N+ CCNC five member rings. In particular bond > stretching, angle bending and torsional parameters. > > Any suggestions appreciated. > > John > University of Colorado at Boulder > > > --Apple-Mail-3--396696999 > Content-Transfer-Encoding: quoted-printable > Content-Type: text/html; > charset=ISO-8859-1 > > -khtml-line-break: after-white-space; ">Folks,

class=3D"khtml-block-placeholder">
Does anyone have experience = > with charged imidazoliums? I am doing molecular dynamic calculations on = > small droplets of ionic liquids. Obviously as the size of the drops = > increases, using quantum methods gets too expensive. However, I have not = > been able to find force field parameters for N+ CCNC five member rings. = > In particular bond stretching, angle bending and torsional = > parameters.=A0

class=3D"khtml-block-placeholder">
Any suggestions = > appreciated.

class=3D"khtml-block-placeholder">
John

style=3D"margin: 0.0px 0.0px 0.0px 0.0px"> size=3D"3" style=3D"font: 12.0px Helvetica">University of Colorado at = > Boulder


class=3D"khtml-block-placeholder">= > > --Apple-Mail-3--396696999--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/+ekFIbqMcl+UPVL4!y7!jqzkJo7+WdEatr9E8jUNFkkT4TAAHf9uI794mQMLTjGJaQ320Ff6hbJ!1b6bphBfPnEJRSe7s+flXPWLulwBO+74CU9ch0DYUzbB75xysHH6DGY791P62HEUNMLbAg4L1vG5e!bFjUXMdRghvvB84VZeWkX8sn0FUQVipYc8KWsUNEcPBPV2UIGcIZeSnKoedcVf9cNpu7OS --=_alternative 0030CCE580257156_= Content-Type: text/html; charset="US-ASCII"
There is a new review article on the subject matter which may be of interest:

Molecular Simulation  
   Publisher:   Taylor & Francis  
   Issue:   Volume 32, Number 01 / January 2006  
   Pages:   1 - 10  
    DOI:   10.1080/08927020500486627  

The simulation of imidazolium-based ionic liquids
P. A. Hunt
Imperial College London, Chemistry Department, London, SW7 2AZ, UK


Gerhard Goldbeck-Wood, PhD
Nanotechnology Consortium Director
Accelrys


"Chris Moth chris.moth*o*vanderbilt.edu" <owner-chemistry+/-ccl.net>
Sent by: owner-chemistry+/-ccl.net

20/04/2006 02:37
Please respond to
"CCL Subscribers" <chemistry+/-ccl.net>
To
"Goldbeck-Wood, Gerhard " <gerhard+/-accelrys.com>
cc
Subject
CCL: Imidazoliums





Sent to CCL by: Chris Moth [chris.moth^^vanderbilt.edu]
You might take a peek at the "HIP" (protonated histidine) residue in the
AMBER force field for some inspiration/validation.

See page 5190 of

Cornell et. al, J. Am. Chem. SOC. 1995, 117, 5179-5197

Though, imidazolium should likely be parameterized in the context of
your particular MD force field.

John Daily john.daily],[colorado.edu wrote:
> Sent to CCL by: John Daily [john.daily,colorado.edu]
>
> --Apple-Mail-3--396696999
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
>                  charset=US-ASCII;
>                  delsp=yes;
>                  format=flowed
>
> Folks,
>
> Does anyone have experience with charged imidazoliums? I am doing  
> molecular dynamic calculations on small droplets of ionic liquids.  
> Obviously as the size of the drops increases, using quantum methods  
> gets too expensive. However, I have not been able to find force field  
> parameters for N+ CCNC five member rings. In particular bond  
> stretching, angle bending and torsional parameters.
>
> Any suggestions appreciated.
>
> John
> University of Colorado at Boulder
>
>
> --Apple-Mail-3--396696999
> Content-Transfer-Encoding: quoted-printable
> Content-Type: text/html;
>                  charset=ISO-8859-1
>
> <HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
> -khtml-line-break: after-white-space; ">Folks,<BR><DIV></DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Does anyone have experience =
> with charged imidazoliums? I am doing molecular dynamic calculations on =
> small droplets of ionic liquids. Obviously as the size of the drops =
> increases, using quantum methods gets too expensive. However, I have not =
> been able to find force field parameters for N+ CCNC five member rings. =
> In particular bond stretching, angle bending and torsional =
> parameters.=A0</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Any suggestions =
> appreciated.</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>John</DIV><DIV><P =
> style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
> size=3D"3" style=3D"font: 12.0px Helvetica">University of Colorado at =
> Boulder</FONT></P> </DIV><BR =
> class=3D"khtml-block-placeholder"></BODY></HTML>=
>
> --Apple-Mail-3--396696999-->
>
>
>
>


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--=_alternative 0030CCE580257156_=-- From owner-chemistry@ccl.net Thu Apr 20 08:19:00 2006 From: "Brian Salter-Duke b_duke%a%bigpond.net.au" To: CCL Subject: CCL: AIM charges - HF or DFT? Message-Id: <-31563-060419225854-3999-iYM6M3jSg3Kpik6ydboLbQ|*|server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 20 Apr 2006 10:32:41 +1000 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke:-:bigpond.net.au] > I have never heard this statement (see below) proffered nor defended. Are > there references to substantiate this statement?? More over, it is truly > difficult to believe that an RHF wavefunction provides a better wavefunction > than say B3LYP (at an identical basis set) for the description of electron > density topology. Are there references to substantiate such an unusual > claim? RHF is the best single determinant wave function using the correct non-relativistic Hamiltonian. These conditions mean it is not necessarily the best wave function. I would prefer the B3LYP orbitals here. Brian. > > Mark > > On 4/17/06, Eduard Matito ematito_-_gmail.com > wrote: > > > > Sent to CCL by: Eduard Matito [ematito=3D=3D=3Dgmail.com] > > Dear David, > > > > > First of all, is a HF or a DFT wave function better? What about the > > > hybrid=3D > > > B3LYP?=3D20=3D20 > > > > > > > > B3LYP geometries are far better than HF ones, but HF is actually the > > best monodeterminantal wavefunction > > by definition, so I would rather consider using HF wavefunction. In > > addition to QTAIM charges a useful tool > > for the analysis of the electron distributions are the so-called > > localization/delocalization indexes (LI and DI). > > See for instance the following papers: > > X. Fradera, M. A. Austen, and R. F. W. Bader, J. Phys. Chem. A, 1999, > > 103, 304. > > J. Poater, M. Sola, M. Duran, and X. Fradera, Theo. Chem. Acc., 2002, > > 107, 362. > > -- Brian Salter-Duke (Brian Duke) b_duke[a]octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. From owner-chemistry@ccl.net Thu Apr 20 08:54:00 2006 From: "Alvyn Liang alvyn.liang=gmail.com" To: CCL Subject: CCL: counterpoise recalculation: read orbitals from checkpoint file? Message-Id: <-31564-060420080734-3993-bVB5DW9DUlvanPFIGAVsNQ|*|server.ccl.net> X-Original-From: "Alvyn Liang" Content-Type: multipart/alternative; boundary="----=_Part_24820_11651799.1145530902715" Date: Thu, 20 Apr 2006 12:01:42 +0100 MIME-Version: 1.0 Sent to CCL by: "Alvyn Liang" [alvyn.liang^_^gmail.com] ------=_Part_24820_11651799.1145530902715 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear all Can anyone tell me how to calculate counterpoise corrected energy from an already optimized structure? Is that possible to use the orbital data insid= e the checkpoint file to accelerate the process? I have met a problem that I had several optimized structure and their checkpoint files. I use the nuclear coordinates to do counterpoise correcte= d energy evaluation but the total energy returned is different from my previous result. I am now trying to use scf=3Dtight to reoptimized it again= , as the previous optimizations are optimized under opt=3Dtight condition. I recon this can be a difference. I an wondering if there is any way to recalculate the counterpoise correcte= d energy using the orbital information inside an optimized checkpoint file? many thanks... Chi-hsiu Liang ------=_Part_24820_11651799.1145530902715 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear all
 
Can anyone tell me how to calculate counterpoise corrected energy from= an already optimized structure? Is that possible to use the orbital data i= nside the checkpoint file to accelerate the process?
 
I have met a problem that I had several optimized structure and their = checkpoint files. I use the nuclear coordinates to do counterpoise correcte= d energy evaluation but the total energy returned is different from my prev= ious result. I am now trying to use scf=3Dtight to reoptimized it again, as= the previous optimizations are optimized under opt=3Dtight condition. I re= con this can be a difference.=20
 
I an wondering if there is any way to recalculate the counterpoise cor= rected energy using the orbital information inside an optimized checkpoint = file?
 
many thanks...
 
Chi-hsiu Liang
------=_Part_24820_11651799.1145530902715-- From owner-chemistry@ccl.net Thu Apr 20 09:29:00 2006 From: "Sudip Chakraborty sudip_c!A!chem.iitkgp.ernet.in" To: CCL Subject: CCL: FORCE FIELD SUGAR MONOMER UNIT Message-Id: <-31565-060419100227-19423-cJ33iu7WORPfWEq0nbDjDQ],[server.ccl.net> X-Original-From: Sudip Chakraborty Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 19 Apr 2006 18:34:19 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Sudip Chakraborty [sudip_c=-=chem.iitkgp.ernet.in] Hi all, Could any one pl inform me how i get the force field of single monomer unit of sugar, which is actually free for academic purpose. Thank in advance sudip -- =========================================================================== | Mr. Sudip Chakraborty | B.C Roy Hall of Residence | | C/o Prof Sanjoy Bandyopadhyay | Room No: NW 105 | | Molecular Modeling Laboratory | | | Department Of Chemistry | | | IIT Kharagpur | | | Kharagpur: 721302 | | | Phone No: 03222283344 | | | Email: sudip_c^chem.iitkgp.ernet.in | | =========================================================================== From owner-chemistry@ccl.net Thu Apr 20 10:56:01 2006 From: "Jan Labanowski janl__speakeasy.net" To: CCL Subject: CCL: Reminders and Thank_You's Message-Id: <-31566-060420105118-21429-6cwTnnXz5SpwvuxTkRdOXA- -server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 20 Apr 2006 14:51:14 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl+*+speakeasy.net] Dear CCL, Time for refreshment course on "Posting to CCL" since I am getting more questions lately. Please read the "Instructions" for CCL at: http://server.ccl.net/chemistry/aboutccl/instructions/index.shtml In short (:-} --- sorry guys, I am not a Lincoln...). 1) If you post to CCL Subscribers either by using the Web form: http://server.ccl.net/cgi-bin/ccl/send_ccl_message or by sending email to: chemistry-$-ccl.net you will need to CONFIRM your posting, i.e., you get an automatic replay from CCL and in this replay message you will be asked to click on the link in the message or to change the message subject and REPLY back. Click or Reply will work the same, provided that you read and do what the message says. While I used to "confirm" messages for you, I do not do it anymore, since there were instances when the message was posted to CCL but was intended as a reply to the original author. So now YOU HAVE TO CONFIRM YOURSELF. I sometimes remind you about the messages waiting for confirmation, so please, do not ignore me: "Send it" or "Delete it". 2) To protect the list from spam, the first time posters to CCL need to be "blessed" by me. That is, you will need to confirm as anyone else, but I will need to accept your message. This is only for first time posts to CCL from a given e-mail address. Once you are "blessed", your own confirmation is enough to post the message to CCL. 3) The CCL will not send messages that have attachments (some attachments are OK, like text/html, but most messages with attachments will be junked). Even the LEGITIMATE attachments, like PGP Signatures will not be let through (NB, some PGP Signatures fakes were used to do buffer overflow on early versions of PGP software). So... If you want to have your message posted, make sure that it does not have attachments. The usual attachments that are stopped, are the infamous "winmail.dat" from MS systems. These have a power of MS-Word and can transmit malicious macros so popular on the most popular operating system. 4) When you respond to CCL mail, it will not go to the author. If you want to respond to the author, read the INSTRUCTIONS. The author e-mail is obfuscated to prevent them from the viruses and spamware that you have in abundance on your beloved MS based systems (I know, I am getting them... Thank you so very much... {:-)}). The Reply should go to the "chemistry-$-ccl.net". If it does not, change the To: line to make it go to "chemistry-$-ccl.net". Some mail agents do not handle the "Reply-To:" header field correctly and will display the "owner-chemistry-$-ccl.net". If you sent mail there, it will be lost forever, since this is the mailbox for bounces and your virus/spamming/whatever_malware that you have on your computers. I do not read the mail sent there, and it is only processed automatically by scripts to unsubscribe bouncing addresses (the bounces go there too...). 5) Some of you may get virus/spam that says that it is from CCL. It is not... Changing the From: field in the header is an old trick of spammers and virus designers. And obviously, they try to put there some address that you would trust. While I cannot say that "CCL will never send you a virus" (if your computer is on the Internet, it will be cracked some day, it is a matter of when, not if, as our beloved leaders tell us...), the CCL does not send spam and virus to my knowledge. I want to use this occasion to thank all of you who use CCL services http://server.ccl.net/chemistry/aboutccl/supporting/index.shtml You are really helping and make this forum run and help all of us. The most popular service is Jobs announcements ( http://www.ccl.net/jobs ). It seems to work for many of you, since you are coming back. Obviously this is a popular site for looking for a job for computer savvy chemists and has a good Google ranking. Use it to post and find good jobs. I also encourage you to use the Conference Listing at: http://server.ccl.net/chemistry/announcements/conferences/index.shtml Find and Post conferences there (posting is free but your support is welcome). Posting your conference/workshop there will make it better attended. Also post the workshops/conferences that you are not associated with, but find useful for the community. Just click on few buttons and cut and paste. I did not finish moving CCL to a new server, so bear with me. I will be gone for two days, and if the current server shuts down, there will be a blackout, since there is no one around to "push the button". Also some messages may be stuck. I will process them when I am back. I may not be on the Internet for most of this period... Sorry... Thank you again for your lively discussions, your personal mail and advice (THANK YOU!!!). I find it very useful and stimulating and will follow up. Keep the CCL running with your submissions, discussions and support. Jan Labanowski CCL Admin jkl-$-ccl.net From owner-chemistry@ccl.net Thu Apr 20 11:30:02 2006 From: "Mgr. Lubos Vrbka lubos.vrbka/a\uochb.cas.cz" To: CCL Subject: CCL: how to prevent rotational motion in MD simulations Message-Id: <-31567-060420105118-12345-ZpbS1JHcdEvvNPl4cDA1KA*server.ccl.net> X-Original-From: "Mgr. Lubos Vrbka" Date: Thu, 20 Apr 2006 07:44:30 +0200 MIME-Version: 1.0 Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka++uochb.cas.cz] hi, > Could anyone point me to either an article describing an algorithm or to > a freely available code that does this? i am sure that gromacs (www.gromacs.org) has the possibility of removing the rotational motion. the algorithm itself is not described in the manual, but you should be able to find it in the sources... regards, lubos -- .................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic http://www.molecular.cz/~vrbka .................................................... [Signature removed by CCL Admin] From owner-chemistry@ccl.net Thu Apr 20 12:05:01 2006 From: "Zengjian Hu huzengjian\a/hotmail.com" To: CCL Subject: CCL: Where to download pdb ligand files? Message-Id: <-31568-060420105339-21870-N0hdDhGilJ/+MtzPCn8uFw]~[server.ccl.net> X-Original-From: "Zengjian Hu" Content-Type: text/plain; format=flowed Date: Thu, 20 Apr 2006 14:06:27 +0000 Mime-Version: 1.0 Sent to CCL by: "Zengjian Hu" [huzengjian]*[hotmail.com] Ask Arthur (Wang Renxiao) in your institute. Hu >From: "Steven Z yzhao_+_mail.sioc.ac.cn" >Reply-To: "CCL Subscribers" >To: "Hu, Zengjian " >Subject: CCL: Where to download pdb ligand files? >Date: Wed, 19 Apr 2006 20:58:47 -0400 > >Sent to CCL by: "Steven Z" [yzhao++mail.sioc.ac.cn] > > >Hi, CCLers > >I'm writing a PDB converting program and I need some diversity structures >to test it. I know that there are about 6400 ligands in Protein Data Bank. >Can anybody tell me where can I download those PDB ligand files? >Thanks in advance. > >Best wishes. > >Steven >============================================================ >State Key Lab of Bio-organic and Natural Products Chemistry >Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of >Sciences. >Addr. 354, Fenglin Road, Shanghai, China. >Tel.: +86-21-54925275 >Email: yzhao.:+:.mail.sioc.ac.cn> > > From owner-chemistry@ccl.net Thu Apr 20 15:05:00 2006 From: "Konstantin Kudin konstantin_kudin_-_yahoo.com" To: CCL Subject: CCL: how to prevent rotational motion in MD simulations Message-Id: <-31569-060420121849-22428-+TjqmewJBQNzeb9ynCiOgQ{=}server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 20 Apr 2006 08:18:41 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin-#-yahoo.com] Hi Ana, It appears that you want to use what is known as "Eckart axis conditions". Use this reference to start chasing down relevant papers: http://dx.doi.org/10.1063/1.1929739 Overall, removing rotations during MD is somewhat tricky. Basically, rotations are defined via a reference structure. So if your system deviates too much from this reference structure, then the degrees of freedom you're removing may be quite far from pure rotations for this current structure in your MD. I hope this helps. Konstantin --- "Ana Celia Araujo Vila Verde avilaverde---engr.psu.edu" wrote: > Sent to CCL by: "Ana Celia Araujo Vila Verde" [avilaverde .. > engr.psu.edu] > This is a multi-part message in MIME format. > > ------_=_NextPart_001_01C663C4.24D82D20 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Hi all, > =20 > I'm doing molecular dynamics simulations of a single polymer chain in > a = > vacuum and the chain is spinning around its centre of mass. The code > I = > use already removes the translation of the centre of mass, but I am = > concerned that too much energy is passed onto the rotational degree > of = > freedom and not enough energy is kept at the vibrational DOFs of the > = > molecule, so I'd like to remove the rotational DOF also during the MD > = > simulation. > =20 > Could anyone point me to either an article describing an algorithm or > to = > a freely available code that does this?=20 > =20 > Thank you, > =20 > Ana Vila Verde > =20 > (Penn State University, Department of Chemical Engineering) > > ------_=_NextPart_001_01C663C4.24D82D20 > Content-Type: text/html; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > DIR=3Dltr> CONTENT=3D"text/html; = > charset=3Diso-8859-1">
color=3D#000000 size=3D2>Hi all,
=0A= >
 
=0A= >
I'm doing molecular dynamics = > simulations of a =0A= > single polymer chain in a vacuum and the chain is spinning around its > = > centre of =0A= > mass. The code I use already removes the translation of the centre of > = > mass, but =0A= > I am concerned that too much energy is passed onto the rotational > degree = > of =0A= > freedom and not enough energy is kept at the vibrational DOFs of > = > the =0A= > molecule, so I'd like to remove the rotational DOF also during the MD > =0A= > simulation.
=0A= >
 
=0A= >
Could anyone point me to either an = > article =0A= > describing an algorithm or to a freely available code that does this? > =0A= >
=0A= >
 
=0A= >
Thank you,
=0A= >
 
=0A= >
Ana Vila Verde
=0A= >
 
=0A= >
(Penn State University, Department > of = > Chemical =0A= > Engineering)
> ------_=_NextPart_001_01C663C4.24D82D20-- > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Thu Apr 20 15:56:00 2006 From: "Rick Venable rvenable-.-pollux.cber.nih.gov" To: CCL Subject: CCL: FORCE FIELD SUGAR MONOMER UNIT Message-Id: <-31570-060420155336-25914-d3BfejHNnC1KBJy5fhjHbg[*]server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 20 Apr 2006 15:47:33 -0400 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable-,-pollux.cber.nih.gov] On Thu, 20 Apr 2006, Sudip Chakraborty sudip_c!A!chem.iitkgp.ernet.in wrote: > Could any one pl inform me how i get the force field of single > monomer unit of sugar, which is actually free for academic purpose. The answer is somewhat program dependent. For AMBER (and progs that can read and use AMBER-style force fields), the GLYCAM force field would be quite useful. See http://glycam.ccrc.uga.edu For CHARMM, esp. for work with other CHARMM parameter sets, CSFF would be my force field of choice. See http://hydrogen.cem.uct.ac.za/compchem/forcefields/ff.htm ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- From owner-chemistry@ccl.net Thu Apr 20 18:43:00 2006 From: "Osman Guner oguner:_:turquoisecons.com" To: CCL Subject: CCL: Second Call for Papers ... ACS - San Francisco Message-Id: <-31571-060420112341-21565-P0GL1OO8xxROfCAbCpILZA(a)server.ccl.net> X-Original-From: "Osman Guner" Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01C66453.B94BE5E0" Date: Thu, 20 Apr 2006 08:23:36 -0700 MIME-Version: 1.0 Sent to CCL by: "Osman Guner" [oguner##turquoisecons.com] This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C66453.B94BE5E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Please note that the deadline for submitting abstracts at the CINF = symposium is May 5th =20 =20 ADVANCES IN VIRTUAL HIGH-THROUGHPUT SCREENING =20 at 232nd ACS National Meeting, San Francisco, CA (September 10-14, 2006) =20 Organized by Chemical Information Division (CINF) Co-sponsored by the Division of Medicinal Chemistry (MEDI) Co-sponsored by the Computers in Chemistry Division (COMP) =20 We invite you to present your recent work in the area of virtual high-throughput screening. We will likely have at least two = subsections: 1- New methods and approaches, and 2- recent applications. Depending on = the level of participation, we may open additional subsections. =20 Topics of interest may include: * 2D structure- or similarity-based database searching=20 * Pharmacophore perception techniques and pharmacophore-based screening * High-throughput docking and scoring * ADME/Tox based screening. =20 Please submit your abstracts through the OASYS (http://oasys.acs.org/acs/232nm/cinf/papers/index.cgi ). The deadline = for submitting the abstract is May 5th. Feel free to contact me for any questions or suggestions. =20 =20 Osman F, G=FCner, PhD Principal, Turquoise Consulting oguner=-=turquoisecons.com=20 http://www.turquoisecons.com=20 =20 ------=_NextPart_000_001C_01C66453.B94BE5E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Please note that = the deadline for submitting abstracts at the CINF symposium is May = 5th

 

 

ADVANCES IN VIRTUAL HIGH-THROUGHPUT SCREENING

 

at 232nd ACS = National Meeting, San = Francisco, CA (September 10-14, = 2006)

 

Organized by = Chemical Information Division (CINF)

Co-sponsored by the = Division of Medicinal Chemistry (MEDI)

Co-sponsored by the Computers in Chemistry Division (COMP)

 

We invite you to = present your recent work in the area of virtual high-throughput screening.=A0 We = will likely have at least two subsections:

1- New methods and approaches, and 2- recent applications.=A0 Depending on the level of participation, we may open additional = subsections.

 

Topics of interest = may include:

*=A0=A0=A0=A0=A0=A0=A0=A0 2D structure- or similarity-based database searching

*=A0=A0=A0=A0=A0=A0=A0=A0 Pharmacophore perception techniques and pharmacophore-based = screening

*=A0=A0=A0=A0=A0=A0=A0=A0 High-throughput docking and scoring

*=A0=A0=A0=A0=A0=A0=A0=A0 ADME/Tox based screening.

 

Please submit your = abstracts through the OASYS (http://oasy= s.acs.org/acs/232nm/cinf/papers/index.cgi ).=A0 The deadline for submitting the abstract is May 5th.=A0 Feel free = to contact me for any questions or suggestions.

 

 

Osman F, G=FCner, PhD

Principal, Turquoise = Consulting

oguner=-=turquoisecons.com&nbs= p;

http://www.turquoisecons.com&nb= sp;

 

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