Jussi, You have a poi= nt here. Let me rephrase my question then:

Can you calcul= ate the Gibbs energy of a system when you are not at a minimum or a TS? In = other words, is there a simple way to calculate a potential GIBBS energy su= rface?

I'm not a specialist on this, but physically havin= g a stretched molecule may only mean being at the geometrical limit of a hi= gh vibrationally state. In principle, there should be an equivalent to E+ZP= E for each point of the curve of a reaction (as long as it is permitted by the uncertainty principle). Can someone share some light on this?

Thanks,

Sebastian

From: "Jussi Lehtola jussi.lehtola,,helsinki.fi" <owne= r-chemistry+/-ccl.net>
To: "Kozuch, Sebastian " <kozuchs+/-yahoo.com>
Sent: Saturday, November 3, 2012 7:= 10 PM
Subject: CCL: ZP= E in non-stationary points

=0A
Sent to CCL by: Ju= ssi Lehtola [jussi.lehtola]^[helsinki.fi]
On Sat, 3 Nov 2012 16:05:34 -0700 (PDT)
"Sebasti= an Kozuch kozuchs]~[yahoo.c= om" <owner-chemistry{:}ccl.net> wrote:
> Dear all,
> = Does anyone know of a (simple) method to calculate ZPE and maybe
> Gi= bbs energies for geometries that are not stationary points (i.e.
> no= t a stable intermediate or a TS)? How valid is a typical frequency
> = calculation for these geometries?

Please elaborate on what you mean.=

Zero point vibrations only make sense in cases where the potential = can
be expanded locally as a Taylor series as
V(r)= ~ V(r0) + (r-r0)*d2V/dr2*(r-r0)
where d2V/dr2 is the Hessian computed a= t r0. This means that you must
be in a stationary point, since the first= derivative (gradient) needs to
vanish.

Secondly, any stationary point will not do, since oth= erwise you will
have a saddle point, meaning that vibrations do not exis= t in some
directions, instead the system is just unstable: when the syst= em is
pushed in this direction, it will not start to oscillate around th= e
configuration in the stationary point, instead the perturbation willjust start growing.

To calculate ZPE you need a bound system. This= is not the case even for
all stationary points -- and even less for non= -stationary points.
--
---------------------------------------------= -----------
Mr. Jussi Lehtola, M. Sc. Doctor= al Student
jussi.lehtola{:}helsinki.fi Depar= tment of Physics
http://www.helsinki.fi/~jzlehtol University of He= lsinki
Office phone: +358 9 191 50 632 Finland
---------------= -----------------------------------------
Jussi Lehtola, FM Tohtorikoulutettava
j= ussi.lehtola{:}helsinki.fi Fysiikan laitos
<= a href=3D"http://www.helsinki.fi/~jzlehtol" target=3D"_blank">http://www.he= lsinki.fi/~jzlehtol Helsingin Yliopisto
Ty=F6puhelin: (0)9 191= 50 632
--------------------------------------------------------

=

-=3D This is automatically added to each message by the mailing scr= ipt =3D-
To recover the email address of the author of the message, plea= se change
the strange characters on the top line to the +/- sign. You can = also
E-mail= to subscribers: CHEMISTRY+/-ccl.net or use:
http:= //www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators:= CHEMISTRY-REQUEST+/-ccl.net or= use
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Before posting, check wait time at= : http://www.ccl.net
Conferences: h= ttp://server.ccl.net/chemistry/announcements/conferences/

Search Mes= sages: http://www.ccl.net/chemistry/searchccl/index.shtml

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--1377744757-1372404203-1352060508=:29950-- From owner-chemistry@ccl.net Sun Nov 4 16:30:00 2012 From: "Arne Dieckmann adieckma%%googlemail.com" To: CCL Subject: CCL: ZPE in non-stationary points Message-Id: <-47842-121104162512-21366-n+Ozm/18DBLnSHt+qIhqcg*server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Sun, 4 Nov 2012 13:25:04 -0800 Mime-Version: 1.0 (1.0) Sent to CCL by: Arne Dieckmann [adieckma]|[googlemail.com] Dear Sebastian, There are ways to do this, but I am not aware of a simple method. You could employ (ab initio) molecular dynamics and use metadynamics, thermodynamic integration or something like that to sample phase space and construct a free energy surface. Cheers, Arne On Nov 4, 2012, at 12:21 PM, "Sebastian Kozuch kozuchs|yahoo.com" wrote: > Jussi, You have a point here. Let me rephrase my question then: > Can you calculate the Gibbs energy of a system when you are not at a minimum or a TS? In other words, is there a simple way to calculate a potential GIBBS energy surface? > I'm not a specialist on this, but physically having a stretched molecule may only mean being at the geometrical limit of a high vibrationally state. In principle, there should be an equivalent to E+ZPE for each point of the curve of a reaction (as long as it is permitted by the uncertainty principle). Can someone share some light on this? > > Thanks, > > Sebastian > > > > ________________________________ > From: "Jussi Lehtola jussi.lehtola,,helsinki.fi" > To: "Kozuch, Sebastian " > Sent: Saturday, November 3, 2012 7:10 PM > Subject: CCL: ZPE in non-stationary points > > > Sent to CCL by: Jussi Lehtola [jussi.lehtola]^[helsinki.fi] > On Sat, 3 Nov 2012 16:05:34 -0700 (PDT) > "Sebastian Kozuch kozuchs]~[yahoo.com" wrote: >> Dear all, >> Does anyone know of a (simple) method to calculate ZPE and maybe >> Gibbs energies for geometries that are not stationary points (i.e. >> not a stable intermediate or a TS)? How valid is a typical frequency >> calculation for these geometries? > > Please elaborate on what you mean. > > Zero point vibrations only make sense in cases where the potential can > be expanded locally as a Taylor series as > V(r) ~ V(r0) + (r-r0)*d2V/dr2*(r-r0) > where d2V/dr2 is the Hessian computed at r0. This means that you must > be in a stationary point, since the first derivative (gradient) needs to > vanish. > > Secondly, any stationary point will not do, since otherwise you will > have a saddle point, meaning that vibrations do not exist in some > directions, instead the system is just unstable: when the system is > pushed in this direction, it will not start to oscillate around the > configuration in the stationary point, instead the perturbation will > just start growing. > > To calculate ZPE you need a bound system. This is not the case even for > all stationary points -- and even less for non-stationary points. > -- > -------------------------------------------------------- > Mr. Jussi Lehtola, M. Sc. Doctoral Student > jussi.lehtola{:}helsinki.fi Department of Physics > http://www.helsinki.fi/~jzlehtol University of Helsinki > Office phone: +358 9 191 50 632 Finland > -------------------------------------------------------- > Jussi Lehtola, FM Tohtorikoulutettava > jussi.lehtola{:}helsinki.fi Fysiikan laitos > http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto > Työpuhelin: (0)9 191 50 632 > --------------------------------------------------------> the strange characters on the top line to the - - sign. You can also > > > E-mail to subscribers: CHEMISTRY- -ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST- -ccl.net or use> > > =--1377744757-1372404203-1352060508=:29950 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: quoted-printable > >

Jussi, You have a point here. Let me rephrase my question then:

Can you calculate the Gibbs energy of a system when you are not at a minimum or a TS? In other words, is there a simple way to calculate a potential GIBBS energy surface?

I'm not a specialist on this, but physically having a stretched molecule may only mean being at the geometrical limit of a high vibrationally state. In principle, there should be an equivalent to E+ZPE for each point of the curve of a reaction (as long as it is permitted by > the uncertainty principle). Can someone share some light on this?

Thanks,

Sebastian

face="Arial" size="2">

From: "Jussi Lehtola jussi.lehtola,,helsinki.fi" <owner-chemistry- -ccl.net>
To: "Kozuch, Sebastian " <kozuchs- -yahoo.com>
Sent: Saturday, November 3, 2012 7:10 PM
Subject: CCL: ZPE in non-stationary points

>
Sent to CCL by: Jussi Lehtola [jussi.lehtola]^[helsinki.fi]
On Sat, 3 Nov 2012 16:05:34 -0700 (PDT)
"Sebastian Kozuch kozuchs]~[yahoo.com" <owner-chemistry{:}ccl.net> wrote:
> Dear all,
> Does anyone know of a (simple) method to calculate ZPE and maybe
> Gibbs energies for geometries that are not stationary points (i.e.
> not a stable intermediate or a TS)? How valid is a typical frequency
> calculation for these geometries?

Please elaborate on what you mean.

Zero point vibrations only make sense in cases where the potential can
be expanded locally as a Taylor series as
V(r) ~ V(r0) + (r-r0)*d2V/dr2*(r-r0)
where d2V/dr2 is the Hessian computed at r0. This means that you must
be in a stationary point, since the first derivative (gradient) needs > to
vanish.

Secondly, any stationary point will not do, since otherwise you will
have a saddle point, meaning that vibrations do not exist in some
directions, instead the system is just unstable: when the system is
pushed in this direction, it will not start to oscillate around the
configuration in the stationary point, instead the perturbation will
just start growing.

To calculate ZPE you need a bound system. This is not the case even for
all stationary points -- and even less for non-stationary points.
--
--------------------------------------------------------
Mr. Jussi Lehtola, M. Sc. Doctoral Student
jussi.lehtola{:}helsinki.fi Department of Physics
http://www.helsinki.fi/~jzlehtol University of Helsinki
Office phone: +358 9 191 50 632 Finland
--------------------------------------------------------
Jussi Lehtola, FM > Tohtorikoulutettava
jussi.lehtola{:}helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632
--------------------------------------------------------

the strange characters on the top line to the - - sign. You can also
E-mail to subscribers: CHEMISTRY- -ccl.net or use:

E-mail to administrators: href="mailto:CHEMISTRY-REQUEST- -ccl.net">CHEMISTRY-REQUEST- -ccl.net or use
http://www.ccl.net/cgi-bin/ccl/send_ccl_message

From owner-chemistry@ccl.net Sun Nov 4 18:05:00 2012 From: "=?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= adrian.cereto .. gmail.com" To: CCL Subject: CCL: Linux performance using a VM appliance Message-Id: <-47843-121104133628-4083-HV0I7/veWiS8HTuUN9QbZw~!~server.ccl.net> X-Original-From: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= Content-Type: multipart/alternative; boundary=f46d044787d33c6e2404cdafa5be Date: Sun, 4 Nov 2012 19:36:01 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= [adrian.cereto%a%gmail.com] --f46d044787d33c6e2404cdafa5be Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Performance will heavily depend on the virtualization software used, on its configuration and on hardware availability of virtualization extensions. I have no experience with Microsoft Windows as a host OS, but maybe others can tell you about that. Adri=C3=A0 2012/11/2 John McKelvey jmmckel-*-gmail.com > > Sent to CCL by: John McKelvey [jmmckel##gmail.com] > Hello.. > > Does anyone have experience running linux QM codes using a Virtual > Machine under Windows? What is your estimate of efficiency using a V > M relative to native code? > > Many thanks, > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel- -gmail.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --f46d044787d33c6e2404cdafa5be Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Performance will heavily depend on the virtualization software used, on its= configuration and on hardware availability of virtualization extensions.
I have no experience with Microsoft Windows as a host OS, but maybe o= thers can tell you about that.

Adri=C3=A0

2012/11/2 John McKelvey jm= mckel-*-gmail.com <owner-chemistry]*[= ccl.net>

Sent to CCL by: John McKelvey [jmmckel##gmail.com]
Hello..

Does anyone have experience running linux QM codes using a Virtual
Machine under Windows? =C2=A0What is your estimate of efficiency using a V<= br> M relative to native code?

Many thanks,

John

--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel- -gmail.com

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY]*[ccl.n= et or use:
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--f46d044787d33c6e2404cdafa5be-- From owner-chemistry@ccl.net Sun Nov 4 18:40:00 2012 From: "TJ O Donnell tjo_-_acm.org" To: CCL Subject: CCL: Linux performance using a VM appliance Message-Id: <-47844-121104183129-808-nUxkbFmo0qo53BW4pJ/AZw(0)server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 4 Nov 2012 15:31:23 -0800 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo ~ acm.org] Although I have not run QM codes in a VM, I've been using VMs for about 5 years now. For computationally intense jobs (docking, clustering large databases, etc.) I get about 85-90% of the speed compared to the native machine. VMs suffer when used for graphical tasks, although they are respectable. Be sure to give the VM as much memory as you can and allow it to use all the processors. I only have experience with VMWare on this front. TJ O'Donnell On Sun, Nov 4, 2012 at 10:36 AM, Adri� Cereto Massagu� adrian.cereto .. gmail.com wrote: > Performance will heavily depend on the virtualization software used, on its > configuration and on hardware availability of virtualization extensions. > > I have no experience with Microsoft Windows as a host OS, but maybe others > can tell you about that. > > Adri� > > 2012/11/2 John McKelvey jmmckel-*-gmail.com >> >> >> Sent to CCL by: John McKelvey [jmmckel##gmail.com] >> Hello.. >> >> Does anyone have experience running linux QM codes using a Virtual >> Machine under Windows? What is your estimate of efficiency using a V >> M relative to native code? >> >> Many thanks, >> >> John >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel- -gmail.com>> E-mail to subscribers: CHEMISTRY-$-ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or use>> >> > From owner-chemistry@ccl.net Sun Nov 4 19:48:00 2012 From: "Frank von Horsten vhorsten{:}phc.uni-kiel.de" To: CCL Subject: CCL: ZPE in non-stationary points Message-Id: <-47845-121104150400-7847-UO+uy+GPj+dHzkThe7sgEw()server.ccl.net> X-Original-From: Frank von Horsten Content-Type: multipart/alternative; boundary=20cf3074d8a4140cb304cdb0de1b Date: Sun, 4 Nov 2012 21:03:50 +0100 MIME-Version: 1.0 Sent to CCL by: Frank von Horsten [vhorsten^phc.uni-kiel.de] --20cf3074d8a4140cb304cdb0de1b Content-Type: text/plain; charset=ISO-8859-1 Hi Sebastian, You should have a look at the paper by Banks and Clary J. Chem. Phys. *130*, 024106 (2009); http://dx.doi.org/10.1063/1.3052076. It deals exactly with the problem of getting ZPEs at non-stationary points, i.e. at geometries where only a subset of DOFs has been optimized while the others are constraint. Hope this helps Frank On 4 November 2012 00:05, Sebastian Kozuch kozuchs]~[yahoo.com < owner-chemistry(0)ccl.net> wrote: > Dear all, > Does anyone know of a (simple) method to calculate ZPE and maybe Gibbs > energies for geometries that are not stationary points (i.e. not a stable > intermediate or a TS)? How valid is a typical frequency calculation for > these geometries? > > Thanks in advance, > Sebastian Kozuch > > --20cf3074d8a4140cb304cdb0de1b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Sebastian,

You should have a look at the paper by Ban= ks and Clary=A0J. Chem. Phys.=A0130, 024106 (2009);=A0http://dx.doi.org/10.1063/1.3052076. It deal= s exactly with the problem of getting ZPEs at non-stationary points, i.e. a= t geometries where only a subset of DOFs has been optimized while the other= s are constraint.

Hope this helps

Frank

On 4 November 2012 00:05, Sebastian Kozuch= kozuchs]~[yahoo.com <= ;owner-chemist= ry(0)ccl.net> wrote:

Dear all,
Does anyone know of a (simple) method to calculate ZPE and maybe Gibb= s energies for geometries that are not stationary points (i.e. not a stable= intermediate or a TS)? How valid is a typical frequency calculation for th= ese geometries?

Thanks in advance,
Sebastian Kozuch