Dear Collea= gues,

As the Guest Editor of a Special Issue of the=C2=A0International Journal of Molecular Scienc= es=C2=A0(IF: 3.687) on "Recent Advances in Virtual Screening"= , it is my pleasure to invite you to submit an article on this topic.=C2=A0= =C2=A0The article may be either a full paper or a com= munication based on your own research in this area, or may be a focused rev= iew article on some aspect of the subject. All submissions will be subject = to peer review.=C2=A0

If you plan to submit a review article e-mail me at gerard.pujadas*o*urv.cat with a title and brief desc= ription at your earliest convenience, in order to avoid multiple reviews co= vering the same material.

For more information about this Special Issue=20 (including acc= epted or in preparation manuscripts), please see:=C2=A0https://w= ww.mdpi.com/journal/ijms/special_issues/virtual_screening=

For inf= ormation on manuscript preparation and related matters, please see the inst= ructions for authors:=C2=A0https://www.mdpi.com/journal/ijms/instructions=

International Journal of Molecular Scie= nces is fully open access.=C2=A0Open access (unlimited an= d free access by readers) increases publicity and promotes more frequent ci= tations, as indicated by several studies.

With best wishes,

Dr. Gerard= Pujadas

<= span style=3D"font-size:10pt">

--000000000000168fd00582507baa-- From owner-chemistry@ccl.net Wed Feb 20 05:41:00 2019 From: "Heribert Reis Hreis\a/eie.gr" To: CCL Subject: CCL:G: MECP optimization Message-Id: <-53620-190220053259-23003-Q5SjJ7Nj5VwV7lG80kgEOA^_^server.ccl.net> X-Original-From: Heribert Reis Content-Type: multipart/alternative; boundary="000000000000308bd0058250e1e3" Date: Wed, 20 Feb 2019 12:32:40 +0200 MIME-Version: 1.0 Sent to CCL by: Heribert Reis [Hreis^eie.gr] --000000000000308bd0058250e1e3 Content-Type: text/plain; charset="UTF-8" Hello, Although ORCA and Columbus are probably better options, I just want to mention that you can use Gaussian as a 'wrapper' for other programs, e.g. GAMESS-US, using the 'external' keyword in the gaussian input file. So you could combine Gaussian's flexible coordinates with GAMESS' CAS capabilities. Heribert On Wed, Feb 20, 2019 at 1:26 AM Hans Lischka hans.lischka[-]univie.ac.at < owner-chemistry:-:ccl.net> wrote: > > Sent to CCL by: Hans Lischka [hans.lischka###univie.ac.at] > Hi Frank, you can use COLUMBUS (https://www.univie.ac.at/columbus/), it > performs the MECP calculations in Pulay coordinates and you can freeze > them in a simple way. You even can do MRCI MECP calculations, depending > on the size of the compounds. The source code is available. > Best, Hans > > On 2/19/2019 8:28 PM, Frank Jensen frj[-]chem.au.dk wrote: > > Sent to CCL by: "Frank Jensen" [frj-#-chem.au.dk] > > I am looking for a quantum chemistry program capable of the following: > > > > Locating minimum energy crossing points (MECP) between states of > different > > spin symmetry using CASSCF wave functions and with additional geometry > > constraints, like fixing bond distances. I in addition need access to the > > program code, as we will need to make some tweaks. > > > > Gamess-US can do MECP, but only in unconstrained Cartesian coordinates. > > Gaussian can in principle do this, but the CASSCF module is not flexible > > enough. > > > >> From the on-line manuals of various other program it is difficult to > infer > > whether geometry constraints are possible in MECP optimizations. > > > > I would appreciate if anybody with experience in running MECP > optimizations > > could point me to possible quantum chemistry programs. > > > > Frank> > > --000000000000308bd0058250e1e3 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hello,

Although ORCA and Columbus are probably better = options, I just want to mention that you can use Gaussian as a 'wrapper= ' for other programs, e.g. GAMESS-US, using the 'external' keyw= ord in the gaussian input file. So you could combine Gaussian's flexibl= e coordinates with GAMESS' CAS capabilities.

H= eribert

On Wed, Feb 20, 2019 at 1:26 AM Hans Lischka hans.lischka[-]univie.ac.at <owner-chemistry:-:ccl.net> wrote:

Sent to CCL by: Hans Lischka [hans.lischka###univie.ac.at]
Hi Frank, you can use COLUMBUS (https://www.univie.ac.at/columbus/= ), it
performs the MECP calculations in Pulay coordinates and you can freeze
them in a simple way. You even can do MRCI MECP calculations, depending on the size of the compounds. The source code is available.
Best, Hans

On 2/19/2019 8:28 PM, Frank Jensen frj[-]chem.au.dk wrote:
> Sent to CCL by: "Frank=C2=A0 Jensen" [frj-#-chem.au.dk]
> I am looking for a quantum chemistry program capable of the following:=
>
> Locating minimum energy crossing points (MECP) between states of diffe= rent
> spin symmetry using CASSCF wave functions and with additional geometry=
> constraints, like fixing bond distances. I in addition need access to = the
> program code, as we will need to make some tweaks.
>
> Gamess-US can do MECP, but only in unconstrained Cartesian coordinates= .
> Gaussian can in principle do this, but the CASSCF module is not flexib= le
> enough.
>
>>=C2=A0 From the on-line manuals of various other program it is diff= icult to infer
> whether geometry constraints are possible in MECP optimizations.
>
> I would appreciate if anybody with experience in running MECP optimiza= tions
> could point me to possible quantum chemistry programs.
>
> Frank>
>

-=3D This is automatically added to each message by the mailing script =3D-=
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--000000000000308bd0058250e1e3-- From owner-chemistry@ccl.net Wed Feb 20 12:43:01 2019 From: "Uche Anene uche#%#uconn.edu" To: CCL Subject: CCL:G: MECP optimization Message-Id: <-53621-190219155459-23338-p40o42lPdD+rB7F+FrnMQg.:.server.ccl.net> X-Original-From: Uche Anene Content-Type: multipart/alternative; boundary="Apple-Mail=_5542A595-F0DC-4FE9-8086-CCCDDD59526F" Date: Tue, 19 Feb 2019 15:54:49 -0500 Mime-Version: 1.0 (Mac OS X Mail 12.2 $3445.102.3$) Sent to CCL by: Uche Anene [uche[a]uconn.edu] --Apple-Mail=_5542A595-F0DC-4FE9-8086-CCCDDD59526F Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii I have run some MECP optimization but not with fixed coordinates. Not = sure if you tried this already, but for GAMESS US try converting to = z-matrix ($ZMAT) to freeze the coordinates. For MECP ($MEX).=20 > On Feb 19, 2019, at 2:28 PM, Frank Jensen frj[-]chem.au.dk = wrote: >=20 >=20 > Sent to CCL by: "Frank Jensen" [frj-#-chem.au.dk] > I am looking for a quantum chemistry program capable of the following: >=20 > Locating minimum energy crossing points (MECP) between states of = different=20 > spin symmetry using CASSCF wave functions and with additional geometry=20= > constraints, like fixing bond distances. I in addition need access to = the=20 > program code, as we will need to make some tweaks. >=20 > Gamess-US can do MECP, but only in unconstrained Cartesian = coordinates. > Gaussian can in principle do this, but the CASSCF module is not = flexible=20 > enough. >=20 >> =46rom the on-line manuals of various other program it is difficult = to infer=20 > whether geometry constraints are possible in MECP optimizations.=20 >=20 > I would appreciate if anybody with experience in running MECP = optimizations=20 > could point me to possible quantum chemistry programs. >=20 > Frank >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20> = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net%2Fcgi-bin%2Fccl%2Fsend_ccl_message&data=3D02%7C01%7Cuche%40uconn.e= du%7Ccfbad51e56944276cb1008d696a8aaf2%7C17f1a87e2a254eaab9df9d439034b080%7= C0%7C0%7C636862048504794488&sdata=3Dy%2BzUdm0e%2Fbk0Nymarm%2BdPOQAuwYK= QUlYVPunkhAKu28%3D&reserved=3D0 >=20> = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net%2Fcgi-bin%2Fccl%2Fsend_ccl_message&data=3D02%7C01%7Cuche%40uconn.e= du%7Ccfbad51e56944276cb1008d696a8aaf2%7C17f1a87e2a254eaab9df9d439034b080%7= C0%7C0%7C636862048504794488&sdata=3Dy%2BzUdm0e%2Fbk0Nymarm%2BdPOQAuwYK= QUlYVPunkhAKu28%3D&reserved=3D0 >=20 > Subscribe/Unsubscribe:=20 > = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net%2Fchemistry%2Fsub_unsub.shtml&data=3D02%7C01%7Cuche%40uconn.edu%7C= cfbad51e56944276cb1008d696a8aaf2%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C= 0%7C636862048504794488&sdata=3D268M%2FIDfrQm8R3FSBqbtum7xIPO83KV96EqfM= fi%2FQa4%3D&reserved=3D0 >=20 > Before posting, check wait time at: = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net&data=3D02%7C01%7Cuche%40uconn.edu%7Ccfbad51e56944276cb1008d696a8aa= f2%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636862048504794488&sda= ta=3Dl1HiKPXxN03pY8YWB3ggNQ9uxd%2BEwBeESPWdkm2JoQM%3D&reserved=3D0 >=20 > Job: = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net%2Fjobs&data=3D02%7C01%7Cuche%40uconn.edu%7Ccfbad51e56944276cb1008d= 696a8aaf2%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636862048504794488&= amp;sdata=3DsUe8U7DUrfgY7DXxlSP4py1IlY%2F5WrnxnB0M7NAFrgk%3D&reserved=3D= 0=20 > Conferences: = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fserver.c= cl.net%2Fchemistry%2Fannouncements%2Fconferences%2F&data=3D02%7C01%7Cu= che%40uconn.edu%7Ccfbad51e56944276cb1008d696a8aaf2%7C17f1a87e2a254eaab9df9= d439034b080%7C0%7C0%7C636862048504794488&sdata=3DqCWIl%2FlWYRtB%2Buyw3= itpgRpFBYcjmfP5uBa%2BsJRBA28%3D&reserved=3D0 >=20 > Search Messages: = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net%2Fchemistry%2Fsearchccl%2Findex.shtml&data=3D02%7C01%7Cuche%40ucon= n.edu%7Ccfbad51e56944276cb1008d696a8aaf2%7C17f1a87e2a254eaab9df9d439034b08= 0%7C0%7C0%7C636862048504794488&sdata=3DCxrjXIG5jO62V%2B%2B8DqiUVQoaeW7= of0lUVDpSC3QLLo4%3D&reserved=3D0 >=20> = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net%2Fspammers.txt&data=3D02%7C01%7Cuche%40uconn.edu%7Ccfbad51e5694427= 6cb1008d696a8aaf2%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C63686204850= 4804501&sdata=3D4PWrBc6kY2MPOAtVmT1%2FMqcWZuxn65qLiAUyCN54e9Y%3D&r= eserved=3D0 >=20 > RTFI: = https://na01.safelinks.protection.outlook.com/?url=3Dhttp%3A%2F%2Fwww.ccl.= net%2Fchemistry%2Faboutccl%2Finstructions%2F&data=3D02%7C01%7Cuche%40u= conn.edu%7Ccfbad51e56944276cb1008d696a8aaf2%7C17f1a87e2a254eaab9df9d439034= b080%7C0%7C0%7C636862048504804501&sdata=3DciUHzPw06ZwkbYRq%2BPzDBZPUHy= SfeY%2FG6hFz7JJ2ELY%3D&reserved=3D0 >=20 >=20 --Apple-Mail=_5542A595-F0DC-4FE9-8086-CCCDDD59526F Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii

I = have run some MECP optimization but not with fixed coordinates. Not sure = if you tried this already, but for GAMESS US try converting to z-matrix = ($ZMAT) to freeze the coordinates. For MECP = ($MEX).

On Feb 19, 2019, at 2:28 PM, Frank Jensen frj[-]chem.au.dk <owner-chemistry===ccl.net> wrote:

Sent to CCL by: "Frank Jensen" [frj-#-chem.au.dk]
I am = looking for a quantum chemistry program capable of the following:

Locating minimum energy crossing points (MECP) = between states of different
spin symmetry using CASSCF = wave functions and with additional geometry
constraints, = like fixing bond distances. I in addition need access to the
program code, as we will need to make some tweaks.

Gamess-US can do MECP, but only in = unconstrained Cartesian coordinates.
Gaussian can in = principle do this, but the CASSCF module is not flexible
enough.

=46rom the on-line manuals of various other program it is = difficult to infer
whether geometry = constraints are possible in MECP optimizations.

I would appreciate if anybody with experience in running MECP = optimizations
could point me to possible quantum = chemistry programs.

Frank

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= --Apple-Mail=_5542A595-F0DC-4FE9-8086-CCCDDD59526F-- From owner-chemistry@ccl.net Wed Feb 20 13:18:01 2019 From: "Siti Khodijah khodijahdanemak[]gmail.com" To: CCL Subject: CCL: I can't open the output gaussian in chemcraft to see the orbital Message-Id: <-53622-190219222310-3934-cISwCrpdtj1+sFWQsg6kXg]_[server.ccl.net> X-Original-From: "Siti Khodijah" Date: Tue, 19 Feb 2019 22:23:08 -0500 Sent to CCL by: "Siti Khodijah" [khodijahdanemak:_:gmail.com] I made an input in avogadro and I used gauusian to calculate the electron density and things, then as a result I could open it through chemcraft but to see the orbital's stuff in chemcraft's tools it could'n open. this is the input: %mem=8gb %nproc=2 #n B3LYP/6-31G(d,p) Opt freq gfprint pop=full iop(6/7=3) isofraxfe 0 1 C -4.31342 4.05922 -0.00000 C -5.50866 3.34330 0.00000 C -5.44984 1.90993 0.00000 C -4.19960 1.24771 0.00000 C -3.07617 3.42549 -0.00000 H -4.35314 5.14266 -0.00000 C -2.98819 2.00891 -0.00000 O -1.73021 1.45765 -0.00000 C -0.60797 2.18940 -0.00000 C -1.83432 4.25668 -0.00000 C -0.63211 3.67068 -0.00000 H -1.90059 5.34036 -0.00000 H 0.28383 4.25139 0.00000 O 0.43197 1.26237 -0.00000 O -6.64232 4.10620 0.00000 O -6.54644 1.11501 0.00000 H -7.46436 1.38480 0.00000 C -7.97204 3.75604 0.00000 H -8.57801 4.68542 -0.00000 H -8.22789 3.20031 0.92640 H -8.22789 3.20031 -0.92640 O -4.24841 -0.11349 0.00000 C -3.20005 -0.99279 -0.00000 H -3.59498 -2.02799 -0.00000 H -2.61167 -0.86181 0.93213 H -2.61167 -0.86181 -0.93213 Fe -0.89132 -0.21019 -0.00000 From owner-chemistry@ccl.net Wed Feb 20 13:53:01 2019 From: "Siti Khodijah khodijahdanemak%%gmail.com" To: CCL Subject: CCL: I can't open the output gaussian in chemcraft to see the orbital Message-Id: <-53623-190219222321-3984-Z++kACqIuFv0PqdvZsMcig^server.ccl.net> X-Original-From: "Siti Khodijah" Date: Tue, 19 Feb 2019 22:23:20 -0500 Sent to CCL by: "Siti Khodijah" [khodijahdanemak[#]gmail.com] I made an input in avogadro and I used gauusian to calculate the electron density and things, then as a result I could open it through chemcraft but to see the orbital's stuff in chemcraft's tools it could'n open. this is the input: %mem=8gb %nproc=2 #n B3LYP/6-31G(d,p) Opt freq gfprint pop=full iop(6/7=3) isofraxfe 0 1 C -4.31342 4.05922 -0.00000 C -5.50866 3.34330 0.00000 C -5.44984 1.90993 0.00000 C -4.19960 1.24771 0.00000 C -3.07617 3.42549 -0.00000 H -4.35314 5.14266 -0.00000 C -2.98819 2.00891 -0.00000 O -1.73021 1.45765 -0.00000 C -0.60797 2.18940 -0.00000 C -1.83432 4.25668 -0.00000 C -0.63211 3.67068 -0.00000 H -1.90059 5.34036 -0.00000 H 0.28383 4.25139 0.00000 O 0.43197 1.26237 -0.00000 O -6.64232 4.10620 0.00000 O -6.54644 1.11501 0.00000 H -7.46436 1.38480 0.00000 C -7.97204 3.75604 0.00000 H -8.57801 4.68542 -0.00000 H -8.22789 3.20031 0.92640 H -8.22789 3.20031 -0.92640 O -4.24841 -0.11349 0.00000 C -3.20005 -0.99279 -0.00000 H -3.59498 -2.02799 -0.00000 H -2.61167 -0.86181 0.93213 H -2.61167 -0.86181 -0.93213 Fe -0.89132 -0.21019 -0.00000 From owner-chemistry@ccl.net Wed Feb 20 14:28:00 2019 From: "Arvydas Tamulis tamulis9 a gmail.com" To: CCL Subject: CCL: What is power and speed of interaction between gravitational field created by molecules of our regular matter and gravitational field created by Dark Matter? Message-Id: <-53624-190220055838-5691-cAH0nZtqKqYESmKuLMUQPw(~)server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: multipart/alternative; boundary="00000000000007e5700582513db1" Date: Wed, 20 Feb 2019 12:58:19 +0200 MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis9]~[gmail.com] --00000000000007e5700582513db1 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Profesor Michel Petitjean, Thank you for your opinion and for your advises. With best regards, Arvydas Tamulis On Tue, Feb 19, 2019 at 11:50 PM Michel Petitjean petitjean.chiral~!~ gmail.com wrote: > > Sent to CCL by: Michel Petitjean [petitjean.chiral=3Dgmail.com] > Dear Arvydas Tamulis, > > I see several questions in your post. > 1. The speed of interacton with a gravitational field. > Looking at https://en.wikipedia.org/wiki/Speed_of_gravity, it seems > that it is speed light in vacuum. > 2. Considering two gravitational fields, like the one of dark matter > and the one of, say, the earth, I assume that their effects are > additive, while I do not know how works the "interaction" between > these two fields. > 3. About the dark matter, I do not know how much there is, and where. > > My advice is that you ask your question in a physics forum. > E.g., https://forum.cosmoquest.org/ > > https://forum.cosmoquest.org/showthread.php?163740-Dark-matter-and-gravit= ational-field-lines > > An other way to operate would that you contact experts: you can find > many names via a Google search. > But I am not sure that there is a clear consensus between experts of > dark matter :) > Good luck. > > Best regards, > > Michel Petitjean > INSERM ERL U1133 (BFA, CNRS UMR 8251), > University Paris 7, > 35 rue Helene Brion, 75205 Paris Cedex 13, France. > Phone: +331 5727 8434; Fax: +331 5727 8372 > E-mail: petitjean.chiral-x-gmail.com (preferred), > michel.petitjean-x-univ-paris-diderot.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.html > > Le mar. 19 f=C3=A9vr. 2019 =C3=A0 18:34, Arvydas Tamulis tamulis9a/gmail.= com > a =C3=A9crit : > > > > Dear Colleagues, > > Would you please inform me what is power and speed of interaction > between gravitational field created by molecules of our regular matter an= d > gravitational field created by Dark Matter? > > I would be appreciate if you send me references on calculations or just > evaluations. > > With best regards, > > Arvydas Tamulis > > > > ***************************************** > > Arvydas Tamulis > > Doctor of Natural Sciences, > > Independent expert of European Commission, > > New website: > https://www.facebook.com/Quantum-entaglement-in-biosystems-39789902708663= 3/timeline/ > > Old website: http://www.itpa.lt/~tamulis/ > > Address: Didlaukio str. 27-40, Vilnius LT-08320, Lithuania > > Emails: tamulis9]![gmail.com or arvydas_tamulis]![yahoo.com > > Tel. +370-69919397 > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --00000000000007e5700582513db1 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Dear Profesor Michel Petitjean,

<= div>Thank you for your opinion and for your advises.

With best regards,

Arvydas Tamulis