Re: [gmx-users] QM/MM in Gromacs-5.1.4?

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

Re: [gmx-users] About the QM/MM MD of Gromacs

rm -rf fort.7 echo 'gets the energies of MM atoms (and other things)' >> QM.stats.log # Guassian uses D rather than e in scientific representation, so we change that. sed 's/D/E/g' temp.7 > fort.7 cat temp.com cat temp.log cat fort.7 cat temp.7 #prints the submission file and result for user

Re: [gmx-users] error message: Invalid transform ...

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 University

[gmx-users] error message: Invalid transform ...

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 Chemistry

Re: [gmx-users] QMMM install on GMX5.1 (Xianchi Dong)

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

Re: [gmx-users] About the QM/MM MD of Gromacs

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) ;else nlines++ }' input

Re: [gmx-users] QM/MM simulations

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 <clintonkin...@chem.byu.edu> wrote: > I'm still working on the same problem I mentioned below. I

Re: [gmx-users] QM/MM simulations

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, Gerrit) > (Clinto

[gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, Gerrit)

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) > &

[gmx-users] QM/MM simulations

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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] interfacing with Gaussian 09

j.abra...@gmail.com> wrote: > > > 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 Cli

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 146, Issue 49

ssian 09 > Message-ID: > < > camnumatzr0defibc_b2b7jhnexkszzqd_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

[gmx-users] interfacing with Gaussian 09

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 -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] How to generate opls aa parameters for new element myself?

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 seeing if they accurately reproduce qm bond lengths, etc. -- Clinton King

[gmx-users] memory error

, 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 any ideas? Thanks.