From owner-chemistry@ccl.net Mon Nov 9 07:58:01 2015 From: "Josh BERRYMAN Josh.Berryman*_*uni.lu" To: CCL Subject: CCL: Question regarding availability of a simulation code Message-Id: <-51868-151109014739-30713-JuMsLzIQO7kCrmgHFaxzNA . server.ccl.net> X-Original-From: Josh BERRYMAN Content-Language: en-JM Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 9 Nov 2015 06:47:31 +0000 MIME-Version: 1.0 Sent to CCL by: Josh BERRYMAN [Josh.Berryman]-[uni.lu] The normal definition of hard spheres is as an infinite potential stepping instantly down to zero at r=.5. That is not compatible with defining forces usefully, so HS simulations are done with event-driven MD rather than the normal fixed-timestep methods. Marcus Bannerman et al.'s DynamO is an open-source event-driven HS code. The best mixing of ED simulations with a continuous potential such as the Coulomb force is not obvious. One approach is to discretise the Coulomb potential, and treat level crossings as a special type of collision. Another approach might be to run fixed-timestep MD with EDMD taking place in between the fixed timesteps. For lengthscales where the HS potential is meaningful (micrometres and up) you might find that you are in low Reynolds-number-land, in which case it is probably quite OK to use a Brownian Dynamics approximation: you can evolve the system using Monte Carlo in this case, with small fixed-size steps in space, thus avoiding the need to define forces. Code for this approach is extremely simple, most groups just write their own see eg. Frenkel & Smit's book, or Allen & Tildesley, both of which have code recipies. Allen & Tildesley is free online as far as I can remember. Josh ________________________________________ > From: owner-chemistry+josh.berryman==uni.lu(0)ccl.net [owner-chemistry+josh.berryman==uni.lu(0)ccl.net] on behalf of Susi Lehtola susi.lehtolaa/alumni.helsinki.fi [owner-chemistry(0)ccl.net] Sent: Sunday, November 08, 2015 05:06 PM To: Josh BERRYMAN Subject: CCL: Question regarding availability of a simulation code Sent to CCL by: Susi Lehtola [susi.lehtola\a/alumni.helsinki.fi] On 11/06/2015 10:04 PM, Rakesh Srivastava allahabad.21::gmail.com wrote: > Dear scholars, > I want to know, is there any MD code available which can simulate a > system of spherical particles which interact via hard sphere and > electrostatic potential. > Thanks in advance. For instance GROMACS (http://www.gromacs.org) can do this, you'd just probably have to use a tabulated potential for your calculation. There was some discussion on the mailing list a few years ago http://comments.gmane.org/gmane.science.biology.gromacs.user/36201 -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola+/-alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Nov 9 08:32:01 2015 From: "Dusan Petrovic dupet100++hhu.de" To: CCL Subject: CCL:G: Ferrocenium cation Message-Id: <-51869-151109080606-14960-bCIx+G3ltLy1bhp6NBoEIA .. server.ccl.net> X-Original-From: "Dusan Petrovic" Date: Mon, 9 Nov 2015 08:06:04 -0500 Sent to CCL by: "Dusan Petrovic" [dupet100|hhu.de] Hi, While the calculation of ferrocene was rather straightforward (B3LYP/6- 311++G** and LANL2DZ for iron), calculation of the ferrocenium ion (Fc+) generates problems. During Fc oxidation, one electron is removed from an orbital that formally belongs to iron (which should change iron's oxidation state from Fe+2 to Fe+3). Therefore, I expected that the partial charge on iron in Fc+ will be close to 1 (it was ~0 in Fc). Geometry optimization works well (I tried B3LYP, M06 and B97D functionals with either pure 6-311++G** or mixed 6-311++G**/ LANL2DZ with ECP in Gaussian). The cation multiplicity was set to 2, as the literature suggests a low spin state. However, calculated ESP charge on iron in Fc+ is negative, while hydrogen atoms have relatively high positive charge. Both restricted and unrestricted open shell calculations show very similar results (-0.033 for C, 0.165 for H and -0.315 for Fe). Contrary to that, semiempirical PM7 partial charges look more reasonable: -0.208 for C, 0.232 for H and 0.753 for Fe. What could be the cause of problems in the DFT calculations? Thanks, Dusan From owner-chemistry@ccl.net Mon Nov 9 10:25:01 2015 From: "Abrash, Samuel sabrash]^[richmond.edu" To: CCL Subject: CCL:G: Ferrocenium cation Message-Id: <-51870-151109100437-24415-vs60m50fEAG6g1LtKO0s8A .. server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 9 Nov 2015 15:04:30 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash~!~richmond.edu] You need to tell us what model you are using to determine the atomic charges. The problem may be with the charge model and not with your calculations. Sent from my iPhone > On Nov 9, 2015, at 9:38 AM, Dusan Petrovic dupet100++hhu.de wrote: > > > Sent to CCL by: "Dusan Petrovic" [dupet100|hhu.de] > Hi, > > While the calculation of ferrocene was rather straightforward (B3LYP/6- > 311++G** and LANL2DZ for iron), calculation of the ferrocenium ion (Fc+) > generates problems. > > During Fc oxidation, one electron is removed from an orbital that formally > belongs to iron (which should change iron's oxidation state from Fe+2 to > Fe+3). Therefore, I expected that the partial charge on iron in Fc+ will be > close to 1 (it was ~0 in Fc). > > Geometry optimization works well (I tried B3LYP, M06 and B97D functionals > with either pure 6-311++G** or mixed 6-311++G**/ LANL2DZ with ECP in > Gaussian). The cation multiplicity was set to 2, as the literature suggests > a low spin state. However, calculated ESP charge on iron in Fc+ is negative, > while hydrogen > atoms have relatively high positive charge. Both restricted and unrestricted > open shell calculations show very similar results (-0.033 for C, 0.165 for H > and -0.315 for Fe). > > Contrary to that, semiempirical PM7 partial charges look more reasonable: > -0.208 for C, 0.232 for H and 0.753 for Fe. > > What could be the cause of problems in the DFT calculations? > > Thanks, > Dusan> > From owner-chemistry@ccl.net Mon Nov 9 20:45:01 2015 From: "Mark Zottola mzottola!A!gmail.com" To: CCL Subject: CCL:G: Ferrocenium cation Message-Id: <-51871-151109204334-1450-DPaXH9MIEG7pNEV28c+ujA : server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=047d7bd76d04247329052425d619 Date: Tue, 10 Nov 2015 08:43:28 +0700 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola~!~gmail.com] --047d7bd76d04247329052425d619 Content-Type: text/plain; charset=UTF-8 Why is there a problem? If you are using Mulliken charges, no one takes those seriously. If you are using electron topology-based methods, there is probably no problem. The formal charge of the ferrocenium ion is 1. It does not mean that the charge of the iron is 1. The overall charge of the molecular species is +1. Just because a result conflicts with your chemical intuition does not mean your intuition is right and the calculation is wrong. I'd say ensure the charge derivation method you are using is appropriate for the level of theory you are using and interpret the results as they are and not what you want them to be. On Mon, Nov 9, 2015 at 8:06 PM, Dusan Petrovic dupet100++hhu.de < owner-chemistry^-^ccl.net> wrote: > > Sent to CCL by: "Dusan Petrovic" [dupet100|hhu.de] > Hi, > > While the calculation of ferrocene was rather straightforward (B3LYP/6- > 311++G** and LANL2DZ for iron), calculation of the ferrocenium ion (Fc+) > generates problems. > > During Fc oxidation, one electron is removed from an orbital that formally > belongs to iron (which should change iron's oxidation state from Fe+2 to > Fe+3). Therefore, I expected that the partial charge on iron in Fc+ will be > close to 1 (it was ~0 in Fc). > > Geometry optimization works well (I tried B3LYP, M06 and B97D functionals > with either pure 6-311++G** or mixed 6-311++G**/ LANL2DZ with ECP in > Gaussian). The cation multiplicity was set to 2, as the literature suggests > a low spin state. However, calculated ESP charge on iron in Fc+ is > negative, > while hydrogen > atoms have relatively high positive charge. Both restricted and > unrestricted > open shell calculations show very similar results (-0.033 for C, 0.165 for > H > and -0.315 for Fe). > > Contrary to that, semiempirical PM7 partial charges look more reasonable: > -0.208 for C, 0.232 for H and 0.753 for Fe. > > What could be the cause of problems in the DFT calculations? > > Thanks, > Dusan> > > --047d7bd76d04247329052425d619 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Why is there a problem?=C2=A0 If you are using Mulliken ch= arges, no one takes those seriously.=C2=A0 If you are using electron topolo= gy-based methods, there is probably no problem.=C2=A0 The formal charge of = the ferrocenium ion is 1.=C2=A0 It does not mean that the charge of the iro= n is 1.=C2=A0 The overall charge of the molecular species is +1.=C2=A0 Just= because a result conflicts with your chemical intuition does not mean your= intuition is right and the calculation is wrong.=C2=A0 I'd say ensure = the charge derivation method you are using is appropriate for the level of = theory you are using and interpret the results as they are and not what you= want them to be.

On Mon, Nov 9, 2015 at 8:06 PM, Dusan Petrovic dupet100++hhu.de <owner-chemistry^-^ccl.net> wro= te:

Sent to CCL by: "Dusan=C2=A0 Petrovic" [dupet100|hhu.de]
Hi,

While the calculation of ferrocene was rather straightforward (B3LYP/6-
311++G** and LANL2DZ for iron), calculation of the ferrocenium ion (Fc+) generates problems.

During Fc oxidation, one electron is removed from an orbital that formally<= br> belongs to iron (which should change iron's oxidation state from Fe+2 t= o
Fe+3). Therefore, I expected that the partial charge on iron in Fc+ will be=
close to 1 (it was ~0 in Fc).

Geometry optimization works well (I tried B3LYP, M06 and B97D functionals with either pure 6-311++G** or mixed 6-311++G**/ LANL2DZ with ECP in
Gaussian). The cation multiplicity was set to 2, as the literature suggests=
a low spin state. However, calculated ESP charge on iron in Fc+ is negative= ,
while hydrogen
atoms have relatively high positive charge. Both restricted and unrestricte= d
open shell calculations show very similar results (-0.033 for C, 0.165 for = H
and -0.315 for Fe).

Contrary to that, semiempirical PM7 partial charges look more reasonable: -0.208 for C, 0.232 for H and 0.753 for Fe.

What could be the cause of problems in the DFT calculations?

Thanks,
Dusan



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