From owner-chemistry@ccl.net Wed May 24 03:48:00 2017
From: "raman kumar raman_chem*_*yahoo.co.in" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: gaussian calculation
Message-Id: <-52810-170523211955-30319-o++VWANh7RaoEs0wAwFCWQ]_[server.ccl.net>
X-Original-From: raman kumar <raman_chem%a%yahoo.co.in>
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Date: Wed, 24 May 2017 01:19:30 +0000 (UTC)
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Sent to CCL by: raman kumar [raman_chem _ yahoo.co.in]
 %nprocshared=4
 %mem=16000MB
 %chk=rh_fc_opt13.chk
 # opt b3lyp/6-31+g(d,p) nosymm scf=(xqc,maxcycle=3000) geom=check  int(grid=ultrafine)
 
 rh_fc_rad_opt13
 
 0  2
 


Regards,
Raman

--------------------------------------------
On Tue, 23/5/17, Martina Cizkova martina.cizkova()ens.fr <owner-chemistry . ccl.net> wrote:

 Subject: CCL:G: gaussian calculation
 To: "Singh, Raman Kumar " <singh . yamanashi.ac.jp>
 Date: Tuesday, 23 May, 2017, 8:46 PM
 
 
 Sent to CCL by: "Martina  Cizkova"
 [martina.cizkova^^^ens.fr]
 Hello, I calculated monocationic
 rhodamine-ferrocene derivative on Gaussian09 with this:
 
 %nprocshared=4
 %mem=16000MB
 %chk=rh_fc_opt13.chk
 # opt b3lyp/6-31+g(d,p) nosymm
 scf=(xqc,maxcycle=3000) formcheck int(grid=ultrafine)
 
 rh_fc_opt13
 
 1 1
 
 It finished without any problem and I
 wanted to calculated monooxidized derivative with previously
 optimized geometry and this:
 
 %nprocshared=4
 %mem=16000MB
 %chk=rh_fc_rad_opt13.chk
 # opt b3lyp/6-31+g(d,p) nosymm
 formcheck int=grid=ultrafine
 scf=(xqc,maxcycle=3000)
 
 rh_fc_rad_opt13
 
 0 2
 
 Unfortunately it failed with this:
 Initial guess <Sx>= 0.0000
 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 0.7500
 S= 0.5000
 Erroneous write. Write 3837952 instead
 of 6325224.
 fd = 4
 orig len = 6325224 left = 6325224
 g_write
  Requested convergence on RMS density
 matrix=1.00D-08 within 128 cycles.
  Requested convergence on MAX density
 matrix=1.00D-06.
  Requested convergence on   
          energy=1.00D-06.
  No special actions if energy rises.
 
 I do not know how to fix it? Can you
 help me with it?
 
 Martina Cizkova
 martina.cizkova|,|ens.fr                    

From owner-chemistry@ccl.net Wed May 24 04:23:00 2017
From: "Igors Mihailovs igorsm ~~ cfi.lu.lv" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: gaussian calculation
Message-Id: <-52811-170524022138-18082-AQM8xQq2kzV6k2+NjhUjfw##server.ccl.net>
X-Original-From: Igors Mihailovs <igorsm/./cfi.lu.lv>
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Date: Wed, 24 May 2017 09:23:07 +0300
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Sent to CCL by: Igors Mihailovs [igorsm(0)cfi.lu.lv]
This is a multi-part message in MIME format.
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Dear Martina Cizkova,

It's just there is no free disk space left. You should delete some 
unneeded files, e.g., old RWFs or checkpoints from Your Scratch directory.

Regards,
Igors Mihailovs
Engineer/PhD student
ISSP UL

On 23/05/17 14:46, Martina Cizkova martina.cizkova()ens.fr wrote:
> Sent to CCL by: "Martina  Cizkova" [martina.cizkova^^^ens.fr]
> Hello, I calculated monocationic rhodamine-ferrocene derivative on Gaussian09 with this:
>
> %nprocshared=4
> %mem=16000MB
> %chk=rh_fc_opt13.chk
> # opt b3lyp/6-31+g(d,p) nosymm scf=(xqc,maxcycle=3000) formcheck int(grid=ultrafine)
>
> rh_fc_opt13
>
> 1 1
>
> It finished without any problem and I wanted to calculated monooxidized derivative with previously optimized geometry and this:
>
> %nprocshared=4
> %mem=16000MB
> %chk=rh_fc_rad_opt13.chk
> # opt b3lyp/6-31+g(d,p) nosymm formcheck int=grid=ultrafine
> scf=(xqc,maxcycle=3000)
>
> rh_fc_rad_opt13
>
> 0 2
>
> Unfortunately it failed with this:
> Initial guess <Sx>= 0.0000 <Sy>= 0.0000 <Sz>= 0.5000 <S**2>= 0.7500 S= 0.5000
> Erroneous write. Write 3837952 instead of 6325224.
> fd = 4
> orig len = 6325224 left = 6325224
> g_write
>   Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
>   Requested convergence on MAX density matrix=1.00D-06.
>   Requested convergence on             energy=1.00D-06.
>   No special actions if energy rises.
>
> I do not know how to fix it? Can you help me with it?
>
> Martina Cizkova
> martina.cizkova|,|ens.fr

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<html>
  <head>
    <meta content="text/html; charset=windows-1252"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    <font face="Liberation Sans">Dear Martina Cizkova,<br>
      <br>
      It's just there is no free disk space left. You should delete some
      unneeded files, e.g., old RWFs or checkpoints from Your Scratch
      directory.<br>
      <br>
      Regards,<br>
      Igors Mihailovs<br>
      Engineer/PhD student<br>
      ISSP UL<br>
    </font><br>
    <div class="moz-cite-prefix">On 23/05/17 14:46, Martina Cizkova
      martina.cizkova()ens.fr wrote:<br>
    </div>
    <blockquote
cite="mid:-id%234fh-52808-170523074700-21618-xl4BbPhSnBsW0hta8Z4hWw],[server.ccl.net"
      type="cite">
      <pre wrap="">Sent to CCL by: "Martina  Cizkova" [martina.cizkova^^^ens.fr]
Hello, I calculated monocationic rhodamine-ferrocene derivative on Gaussian09 with this:

%nprocshared=4
%mem=16000MB
%chk=rh_fc_opt13.chk
# opt b3lyp/6-31+g(d,p) nosymm scf=(xqc,maxcycle=3000) formcheck int(grid=ultrafine)

rh_fc_opt13

1 1

It finished without any problem and I wanted to calculated monooxidized derivative with previously optimized geometry and this:

%nprocshared=4
%mem=16000MB
%chk=rh_fc_rad_opt13.chk
# opt b3lyp/6-31+g(d,p) nosymm formcheck int=grid=ultrafine
scf=(xqc,maxcycle=3000)

rh_fc_rad_opt13

0 2

Unfortunately it failed with this:
Initial guess &lt;Sx&gt;= 0.0000 &lt;Sy&gt;= 0.0000 &lt;Sz&gt;= 0.5000 &lt;S**2&gt;= 0.7500 S= 0.5000
Erroneous write. Write 3837952 instead of 6325224.
fd = 4
orig len = 6325224 left = 6325224
g_write
 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
 Requested convergence on MAX density matrix=1.00D-06.
 Requested convergence on             energy=1.00D-06.
 No special actions if energy rises.

I do not know how to fix it? Can you help me with it?

Martina Cizkova
martina.cizkova|,|ens.fr
</pre>
    </blockquote>
  </body>
</html>

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From owner-chemistry@ccl.net Wed May 24 09:17:00 2017
From: "Nick Green nicogreen6() gmail.com" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: MM3 parameters
Message-Id: <-52812-170524091529-13635-brNGcuyqZb4KfyR2R1BrMA-$-server.ccl.net>
X-Original-From: "Nick  Green" <nicogreen6 : gmail.com>
Date: Wed, 24 May 2017 09:15:28 -0400


Sent to CCL by: "Nick  Green" [nicogreen6*|*gmail.com]
Dear Colleagues,

I have always performed conformational searches using mm+ via Hyperchem or MMFF 
via Spartan on an i7.
Due to the increase of complexity of the molecules I am working at the moment, 
I am using Tinker on a Cluster.
Unfortunately I am working with atom types that are not fully parameterized for 
mm3 (the forcefield I am testing at the moment).
Does anyone know a list, manuscript or somewhere where I may find an extended 
list of parameters beyond the mm3(2000)?

Regards,

Nick


From owner-chemistry@ccl.net Wed May 24 15:13:00 2017
From: "Marcos Verissimo Alves marcos_verissimo:-:id.uff.br" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: LJ parameters for Gromacs/Orca QM/MM calculation
Message-Id: <-52813-170524151218-32249-IJU5tTo3Ph5S+qd0mwNyPw-#-server.ccl.net>
X-Original-From: Marcos Verissimo Alves <marcos_verissimo .. id.uff.br>
Content-Type: multipart/alternative; boundary="001a114e61b8a9a7e6055049e183"
Date: Wed, 24 May 2017 16:11:32 -0300
MIME-Version: 1.0


Sent to CCL by: Marcos Verissimo Alves [marcos_verissimo^_^id.uff.br]
--001a114e61b8a9a7e6055049e183
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Hello,

I am learning how to perform QM/MM calculations using Gromacs and Orca. I
have already managed to run a calculation from a simple tutorial, but I
have some doubts (not all of them specific to the Gromacs/Orca duo), and I
hope someone more knowledgeable than I can help me.

1) As far as I can tell, Orca only takes vdW interactions into account (via
LJ parameters of the force fields)  if a full QM/MM optimization is
performed for each MD step - the LJ parameter files only appear if the
option for a full geometry otimization of the QM part is set. Is there any
way to make Orca take the LJ parameters into account if a single-point
calculation is performed?

2) If there is no way to do it just by setting flags in Gromacs, is there
some way to go around this? Some effective way of making he QM and MM
regions be taken into account when calculating the total energy of the QM +
MM system?

3) Now a more fundamental question, not exactly related to Gromacs or Orca,
but to QM/MM itself. In which situations (in a general way) would the
neglect of LJ interactions between the two sub-regions be acceptable, and
which would be not?

Best regards,

---

Dr. Marcos Verissimo Alves
Prof. Adjunto II, Curso de F=C3=ADsica Computacional
Instituto de Ci=C3=AAncias Exatas
Universidade Federal Fluminense
Volta Redonda - RJ, Brasil

--001a114e61b8a9a7e6055049e183
Content-Type: text/html; charset="UTF-8"
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<div dir=3D"ltr">Hello,<div><br></div><div>I am learning how to perform QM/=
MM calculations using Gromacs and Orca. I have already managed to run a cal=
culation from a simple tutorial, but I have some doubts (not all of them sp=
ecific to the Gromacs/Orca duo), and I hope someone more knowledgeable than=
 I can help me.</div><div><br></div><div>1) As far as I can tell, Orca only=
 takes vdW interactions into account (via LJ parameters of the force fields=
)=C2=A0=C2=A0if a full QM/MM optimization is performed for each MD step - t=
he LJ parameter files only appear if the option for a full geometry otimiza=
tion of the QM part is set. Is there any way to make Orca take the LJ param=
eters into account if a single-point calculation is performed?</div><div><b=
r></div><div>2) If there is no way to do it just by setting flags in Gromac=
s, is there some way to go around this? Some effective way of making he QM =
and MM regions be taken into account when calculating the total energy of t=
he QM + MM system?</div><div><br></div><div>3) Now a more fundamental quest=
ion, not exactly related to Gromacs or Orca, but to QM/MM itself. In which =
situations (in a general way) would the neglect of LJ interactions between =
the two sub-regions be acceptable, and which would be not?</div><div><br></=
div><div>Best regards,</div><div><br></div><div><div><div class=3D"gmail_si=
gnature"><div dir=3D"ltr"><div><div dir=3D"ltr"><div dir=3D"ltr"><div dir=
=3D"ltr"><div dir=3D"ltr"><div>---</div><div><br></div>Dr. Marcos Verissimo=
 Alves<div>Prof. Adjunto II, Curso de F=C3=ADsica Computacional</div><div><=
span style=3D"font-size:12.8px">Instituto de Ci=C3=AAncias Exatas</span><br=
></div><div>Universidade Federal Fluminense</div><div>Volta Redonda - RJ, B=
rasil<br></div></div></div></div></div></div></div></div></div>
</div></div>

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