Hello Conor,

There are two issues here:= first, you did not convert Angstrom to nanometers when constructing your .= gro files. Second=E2=80=94and most important=E2=80=94your atom types and th= e resulting connectivity is incorrect. For example, you have HC (atom 8) ne= ar O (atom 3) in your original structure, but what you intended was to have= HO near OH. You could simply rename the atoms and correct the connectivity= in the tinker xyz. A correct .gro file would look like the following:

=C2=A0Molecular System

=C2=A0 =C2=A0 8<= /div>

=C2=A0 =C2=A0 1 =C2=A0TTA =C2=A0C =C2=A0 =C2=A0 =C2=A01 =C2=A0 0.= 000 =C2=A0 0.476 =C2=A0 0.839

=C2=A0 =C2=A0 1 =C2=A0TTA =C2=A0CT = =C2=A0 =C2=A0 2 =C2=A0 0.002 =C2=A0 0.325 =C2=A0 0.838

=C2=A0 =C2= =A0 1 =C2=A0TTA =C2=A0OH =C2=A0 =C2=A0 3 =C2=A0 0.115 =C2=A0 0.544 =C2=A0 0= .838

=C2=A0 =C2=A0 1 =C2=A0TTA =C2=A0O =C2=A0 =C2=A0 =C2=A04 =C2= =A0-0.105 =C2=A0 0.535 =C2=A0 0.839

=C2=A0 =C2=A0 1 =C2=A0TTA =C2= =A0HC =C2=A0 =C2=A0 5 =C2=A0 0.105 =C2=A0 0.290 =C2=A0 0.837

=C2= =A0 =C2=A0 1 =C2=A0TTA =C2=A0HC =C2=A0 =C2=A0 6 =C2=A0-0.048 =C2=A0 0.287 = =C2=A0 0.927

=C2=A0 =C2=A0 1 =C2=A0TTA =C2=A0HC =C2=A0 =C2=A0 7 = =C2=A0-0.050 =C2=A0 0.288 =C2=A0 0.749

=C2=A0 =C2=A0 1 =C2=A0TTA = =C2=A0HO =C2=A0 =C2=A0 8 =C2=A0 0.114 =C2=A0 0.641 =C2=A0 0.838

= =C2=A0 50.00000 =C2=A050.00000 =C2=A050.00000

=C2= =A0Cheers

On Tue, Dec 16, 2014 at 10:58 AM, conor douglas parks coparks2012= /agmail.com <owner-chemistry%x%ccl.n= et> wrote:

Sent to CCL by: "conor douglas parks" [coparks2012:-:gmail.com]
Hello,

I am trying to perform a simple energy minimization of Acetic acid using ne= wton.x from Tinker. I am getting very bogus results, and I cannot figure ou= t what the source of the error is. I have chosen Acetic acid to test, becau= se all the parameters exist in the oplsaa.prm file. Here is my input coordi= nate file in tinker xyz file format. This consists of the PDB file coordina= tes translated and rotated into my simulation box.

=C2=A0 =C2=A0 =C2=A08
=C2=A0 =C2=A0 =C2=A01=C2=A0 CT=C2=A0 =C2=A0 =C2=A00.001179=C2=A0 =C2=A0 4.7= 56225=C2=A0 =C2=A0 8.385862=C2=A0 =C2=A0 80=C2=A0 =C2=A0 =C2=A02=C2=A0 =C2= =A0 =C2=A06=C2=A0 =C2=A0 =C2=A07=C2=A0 =C2=A0 =C2=A08
=C2=A0 =C2=A0 =C2=A02=C2=A0 C=C2=A0 =C2=A0 =C2=A0 0.021679=C2=A0 =C2=A0 3.2= 49325=C2=A0 =C2=A0 8.377562=C2=A0 =C2=A0209=C2=A0 =C2=A0 =C2=A01=C2=A0 =C2= =A0 =C2=A03=C2=A0 =C2=A0 =C2=A04
=C2=A0 =C2=A0 =C2=A03=C2=A0 O=C2=A0 =C2=A0 =C2=A0 1.154379=C2=A0 =C2=A0 5.4= 43125=C2=A0 =C2=A0 8.378562=C2=A0 =C2=A0210=C2=A0 =C2=A0 =C2=A02
=C2=A0 =C2=A0 =C2=A04=C2=A0 OH=C2=A0 =C2=A0 -1.053221=C2=A0 =C2=A0 5.346025= =C2=A0 =C2=A0 8.394062=C2=A0 =C2=A0211=C2=A0 =C2=A0 =C2=A02=C2=A0 =C2=A0 = =C2=A05
=C2=A0 =C2=A0 =C2=A05=C2=A0 HO=C2=A0 =C2=A0 =C2=A01.054079=C2=A0 =C2=A0 2.9= 00025=C2=A0 =C2=A0 8.365862=C2=A0 =C2=A0212=C2=A0 =C2=A0 =C2=A04
=C2=A0 =C2=A0 =C2=A06=C2=A0 HC=C2=A0 =C2=A0 -0.478721=C2=A0 =C2=A0 2.874325= =C2=A0 =C2=A0 9.270362=C2=A0 =C2=A0 85=C2=A0 =C2=A0 =C2=A01
=C2=A0 =C2=A0 =C2=A07=C2=A0 HC=C2=A0 =C2=A0 -0.495721=C2=A0 =C2=A0 2.883825= =C2=A0 =C2=A0 7.490562=C2=A0 =C2=A0 85=C2=A0 =C2=A0 =C2=A01
=C2=A0 =C2=A0 =C2=A08=C2=A0 HC=C2=A0 =C2=A0 =C2=A01.141279=C2=A0 =C2=A0 6.4= 10025=C2=A0 =C2=A0 8.383862=C2=A0 =C2=A0 85=C2=A0 =C2=A0 =C2=A01

Here it is in .gro file format, if you would like to view in VMD to see tha= t it is the correct conformation

=C2=A0Molecular System
=C2=A0 =C2=A0 8
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 CT=C2=A0 =C2=A0 =C2=A01=C2=A0 =C2=A00.001= =C2=A0 =C2=A04.756=C2=A0 =C2=A08.386
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 C=C2=A0 =C2=A0 =C2=A0 2=C2=A0 =C2=A00.022= =C2=A0 =C2=A03.249=C2=A0 =C2=A08.378
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 O=C2=A0 =C2=A0 =C2=A0 3=C2=A0 =C2=A01.154= =C2=A0 =C2=A05.443=C2=A0 =C2=A08.379
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 OH=C2=A0 =C2=A0 =C2=A04=C2=A0 -1.053=C2=A0 = =C2=A05.346=C2=A0 =C2=A08.394
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HO=C2=A0 =C2=A0 =C2=A05=C2=A0 =C2=A01.054= =C2=A0 =C2=A02.900=C2=A0 =C2=A08.366
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HC=C2=A0 =C2=A0 =C2=A06=C2=A0 -0.479=C2=A0 = =C2=A02.874=C2=A0 =C2=A09.270
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HC=C2=A0 =C2=A0 =C2=A07=C2=A0 -0.496=C2=A0 = =C2=A02.884=C2=A0 =C2=A07.491
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HC=C2=A0 =C2=A0 =C2=A08=C2=A0 =C2=A01.141= =C2=A0 =C2=A06.410=C2=A0 =C2=A08.384
=C2=A0 50.00000=C2=A0 50.00000=C2=A0 50.00000

I ran ./newton.x tinker_xyz.xyz oplsaa.prm newton none 0.001

The minimized structure output in .gro file format for viewing is

=C2=A0Molecular System
=C2=A0 =C2=A0 8
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 CT=C2=A0 =C2=A0 =C2=A01=C2=A0 =C2=A00.062= =C2=A0 =C2=A03.705=C2=A0 =C2=A09.003
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 C=C2=A0 =C2=A0 =C2=A0 2=C2=A0 =C2=A00.350= =C2=A0 =C2=A04.708=C2=A0 =C2=A07.893
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 O=C2=A0 =C2=A0 =C2=A0 3=C2=A0 =C2=A01.367= =C2=A0 =C2=A05.392=C2=A0 =C2=A07.823
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 OH=C2=A0 =C2=A0 =C2=A04=C2=A0 -0.661=C2=A0 = =C2=A04.755=C2=A0 =C2=A06.985
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HO=C2=A0 =C2=A0 =C2=A05=C2=A0 -1.358=C2=A0 = =C2=A04.160=C2=A0 =C2=A07.204
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HC=C2=A0 =C2=A0 =C2=A06=C2=A0 =C2=A00.688= =C2=A0 =C2=A03.457=C2=A0 =C2=A09.861
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HC=C2=A0 =C2=A0 =C2=A07=C2=A0 =C2=A00.895= =C2=A0 =C2=A03.123=C2=A0 =C2=A08.605
=C2=A0 =C2=A0 1=C2=A0 TTA=C2=A0 HC=C2=A0 =C2=A0 =C2=A08=C2=A0 =C2=A00.001= =C2=A0 =C2=A04.563=C2=A0 =C2=A09.674
=C2=A0 50.00000=C2=A0 50.00000=C2=A0 50.00000

As you can see, the molecular geometry is completely wrong. I cannot seem t= o figure out why the newton code is doing this. Also, if I run ./minimiz.x = tinker_xyz.xyz oplsaa.prm 0.001, I get a termination due to small fct. Why = cant the minimization code handle the PDB file coordinates as an input?

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William J. McDonald
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Department of= Chemistry and Biochemistry
University of California, Santa Cruz

--001a113389a0194f0c050a5c0bf7-- From owner-chemistry@ccl.net Tue Dec 16 19:28:01 2014 From: "Lars Goerigk lars.goerigk~~unimelb.edu.au" To: CCL Subject: CCL:G: MP2 Geom. optimization oscillation Message-Id: <-50828-141216181430-5639-atTEh51E+jvLlrTmx1LfZg]_[server.ccl.net> X-Original-From: Lars Goerigk Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_8C743283C6684C8781B2076A66572DAAunimelbeduau_" Date: Tue, 16 Dec 2014 23:13:02 +0000 MIME-Version: 1.0 Sent to CCL by: Lars Goerigk [lars.goerigk[]unimelb.edu.au] --_000_8C743283C6684C8781B2076A66572DAAunimelbeduau_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear Mi, I would suggest to not use MP2 for these optimizations, particularly becaus= e MP2 overestimates dispersion interactions in non-covalently bound complex= es. Moreover, I presume you are limited to a small basis set with MP2, which furthermore introduces a significant contribution of basis-= set-superposition error which further affects the quality of your geometrie= s. It has been shown in the literature that for single-point calculations and = geometry optimizations of organic complexes, dispersion-correced DFT with a= triple-zeta basis is a much more accurate and computationally efficient ap= proach. This is particularly true if you use Grimme=92s DFT-D3 correction with Beck= e-Johnson damping. If you are restricted to Gaussian, you could use TPSS or B3LYP with DFT-D3(= BJ) (keyword EmpiricalDispersion=3DGD3BJ) If you have access to Turbomole or ORCA (which is a free program) I also re= commend Truhlar=92s PW6B95 functional which provides very accurate geometri= es. As I said before you can expect a higher accuracy for such complexes than w= ith MP2/DZ or MP2/TZ. Recent papers on DFT-D3(BJ) and accurate geometries are: J. Comput. Chem. 2011, 32, 1456. PCCP 2013, 15, 16031. JCTC 2013, 9, 3240. Cheers, Lars --- Dr. Lars Goerigk ARC DECRA Fellow School of Chemistry The University of Melbourne VIC 3010 Australia Research profile: http://www.chemistry.unimelb.edu.au/dr-lars-goerigk List of my publications: http://www.researcherid.com/rid/D-3717-2009 On 17 Dec 2014, at 7:05 am, Mi Yang agri_chemist---yahoo.com

> wrote: Sent to CCL by: "Mi Yang" [agri_chemist(_)yahoo.com] Dear CCL colleagues, I am optimizing a complex (about 30 organic atoms) with 3 water molecules. = BUT unfortunately optimization goes to near convergence and starts oscillations and keep on o= scillating I have tried several possible procedures to get the job finish but all in v= ain. For instance, I have stopped the job and slightly changed the geom. and run it again. Similarly,= I have also optimized the complex with B3LYP first and hv taken guess from there to perform MP2 optim= ization but none of these tactics worked. How I can get rid of these oscillations at MP2 method (while other methods = do not have any such problems)..? Mi -=3D This is automatically added to each message by the mailing script =3D-E-mail to subscribers: CHEMISTRY!A!ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_8C743283C6684C8781B2076A66572DAAunimelbeduau_ Content-Type: text/html; charset="Windows-1252" Content-ID: <2F0104D70970B84CAA417501772BF3FD!A!unimelb.edu.au> Content-Transfer-Encoding: quoted-printable Dear Mi,

I would suggest to not use MP2 for these optimizations, particularly b= ecause MP2 overestimates dispersion interactions in non-covalently bound co= mplexes. Moreover, I presume you are limited to a small basis set

with MP2, which furthermore introduces a significant contribution of b= asis-set-superposition error which further affects the quality of your geom= etries.

It has been shown in the literature that for single-point calculations= and geometry optimizations of organic complexes, dispersion-correced DFT w= ith a triple-zeta basis is a much more accurate and computationally efficie= nt approach.

This is particularly true if you use Grimme=92s DFT-D3 correction with= Becke-Johnson damping.

If you are restricted to Gaussian, you could use TPSS or B3LYP with DF= T-D3(BJ) (keyword EmpiricalDispersion=3DGD3= BJ)

If you have access to Turbomole or ORCA (which is a free program) I al= so recommend Truhlar=92s PW6B95 functional which provides very accurate geo= metries.

As I said before you can expect a higher accuracy for such complexes t= han with MP2/DZ or MP2/TZ.

Recent papers on DFT-D3(BJ) and accurate geometries are:

J. Comput. Chem. 2011, 32, 1456.

PCCP 2013, 15, 16031.

JCTC 2013, 9, 3240.

Cheers,

Lars

---

Dr. Lars Goerigk

ARC DECRA Fellow

School of Chemistry

The University of Melbourne

VIC 3010

Australia

Research profile:

http://www.= chemistry.unimelb.edu.au/dr-lars-goerigk

List of my publications:

http://www.research= erid.com/rid/D-3717-2009

On 17 Dec 2014, at 7:05 am, Mi Yang agri_chemist---yahoo.com <owne= r-chemistry!A!ccl.net> wrote:

Sent to CCL by: "Mi Yang" [agri_chemist(_)yahoo.com]
Dear CCL colleagues,

I am optimizing a complex (about 30 organic atoms) with 3 water molecules. = BUT unfortunately
optimization goes to near convergence and starts oscillations and keep on o= scillating
I have tried several possible procedures to get the job finish but all in v= ain. For instance, I have
stopped the job and slightly changed the geom. and run it again. Similarly,= I have also optimized the
complex with B3LYP first and hv taken guess from there to perform MP2 optim= ization but none of
these tactics worked.
How I can get rid of these oscillations at MP2 method (while other methods = do not have any such
problems)..?

Mi

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