entry for Quantum En. is 0.000.
Has anyone else seen this problem before? If so, what did you do about it?
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
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Is is true that the gau script available at http://wwwuser.gwdg.de/~
ggroenh/qmmm.html only works with gromacs versions < 5?
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
>
>
>5. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit)
>
> Hi
446
6 54.1258397 21.0589621 26.8486065
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
On Thu, Sep 1, 2016 at 7:03 AM, wrote:
>
> Today's Topics:
>
>1. Re: QM/MM simulations (Mark Abraham) (Groenhof, G
Nevermind, I figured out the answer to this question. Thanks!
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
On Wed, Sep 7, 2016 at 1:14 PM, Clinton King
wrote:
> I'm still working on the same problem I mentioned below. I'm trying to
> verify
wants to
use it.
awk -v nlines=0 '{if (nlines > 2 && $1) printf "%10.8f %10.8f %10.8f\n",
$2*0.529177249,$3*0.529177249,$4*0.529177249}{if ($1) ;else nlines++ }'
input.com >> temp.com
awk -v nlines=0 '{if (nlines > 2 && $1) print $1}{if ($1) ;el
Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
You will also need to set the following variable at install time:
-DGMX_QMMM_MOPAC=ON
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
>
>1. QMMM install on GMX5.1 (Xianch
but in the output I see this message:
"number of CPUs for gaussian = 1
memory for gaussian = 5000"
and then I get a memory error.
I don't see any description of keywords in the manual to set the memory in
the mdp file, but maybe I'm missing something. Does anybody have a
e (you'll have to dig into the literature, maybe you
can find solvated structures or a radial distribution function) and then
adjusting the parameters until the experimental value is reproduced. You
could also benchmark the molecular mechanics parameters against a
higher-level qm computation by
I'm having difficulty interfacing GROMACS with Gaussian 09. Is there anyone
who has successfully done it who is willing to give some advice?
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
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Gromacs Users mailing list
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husemo6f_n-obw...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Please check out http://wwwuser.gwdg.de/~ggroenh/qmmm.html and
> http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM
>
> Mark
>
> On Fri, Jun 10, 2
;
> > Hi,
> >
> > Please check out http://wwwuser.gwdg.de/~ggroenh/qmmm.html and
> >
> http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM
> >
> > Mark
> >
> > On Fri, Jun 10, 2016 at 5:13 PM Clinton King >
> &
ring
https://drive.google.com/file/d/0B-W4G39j_IcjZlVPb1NySkUtRDQ/view?usp=sharing
(Please let me know if the links above don't work.)
Thanks for your help
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
> Message: 2
> Date: Sun, 12 Jun 2016 05:16:13 +
> From:
Has anybody ever seen the following error message before?
Program: gmx mdrun, version 2016.1
Source file: src/gromacs/fft/parallel_3dfft.cpp (line 173)
*Fatal error:*
*Invalid transform. Plan and execution don't match regarding reel/complex*
--
Clinton King
Graduate Student
Chem
ded
a gaussian keyword to allow the gaussian computation steps to tolerate
close interatomic distances. I will continue to troubleshoot and send an
update post if I learn any more about what might have caused this error
message.
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young Unive
rs from Gaussian need to be
multiplied by 2.0155295489e-5, but this is taken care of in the gromacs code
paste MMcharges.txt gradients.txt|awk '{if ($3 == "Atom") print
-1*$1*$5,-1*$1*$6,-1*$1*$7; else print -1*$1*$4,-1*$1*$5,-1*$1*$6}' |
column -t >> temp.7
#prints the fort.7 b
Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html
Also, you need to set the following variable at compile time
-DGMX_QMMM_ORCA=ON
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
> Message: 3
> Date: Wed, 2 Aug 2017 15:01:29 +0200
> Fro
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