Re: [gmx-users] QM/MM simulations

ng University > > On Thu, Sep 1, 2016 at 7:03 AM, @maillist.sys.kth.se> wrote: > >> >> Today's Topics: >> >>1. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) >> (Clinton King) (Groenhof, Gerrit) >> ----

Re: [gmx-users] QM/MM simulations

errit) > (Clinton King) (Groenhof, Gerrit) > -- > > Message: 1 > Date: Thu, 1 Sep 2016 10:08:19 + > From: "Groenhof, Gerrit" > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-us

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

1 Aug 2016 13:28:56 -0600 From: Clinton King To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) Message-ID: Content-Type: text/plain; charset=UTF-8 Is is true that the gau script available at http://wwwuser.gw

[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) > > Hi, > > Unless there

Re: [gmx-users] QM/MM simulations (Mark Abraham)

Hi, Unless there are no atoms in the QM region, the QM energy should not be zero. Can you confirm that mdrun writes an input file (input.com)? and gaussian is executed? If not, has gromacs been compiled with QMMM support (GMX_QMMM_PROGRAM:STRING=gaussian)? Best, Gerrit Hi, Sadly, most of

Re: [gmx-users] QM/MM simulations

Hi, Sadly, most of the QM/MM interfaces have been lacking a maintainer on the GROMACS side for quite a number of years. You should definitely be following http://wwwuser.gwdg.de/~ggroenh/qmmm.html closely. Mark On Mon, Aug 29, 2016 at 9:36 PM Clinton King wrote: > I'm performing a QM/MM (using

[gmx-users] QM/MM simulations

I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation of a single molecule of octanol in a box of water. In examining the standard output, it appears that call to Gaussian is proceeding as expected, but looking at the log file, it doesn't appear that quantum energy is being commun

Re: [gmx-users] QM/MM simulations

On 4/29/14, 4:46 AM, Iamkaant wrote: So, I'v made a little test run based on slightly modified tutorial files. As far as I can judge, mdrun operates properly, ORCA is called and also works OK. Here is zipped working directory

Re: [gmx-users] QM/MM simulations

ORCA optimization with the same input file converged in 9 minutes. Probably it is due to different CPU loads -- during QM/MM each of 16 CPUs was loaded on ca 6 %, when ORCA ran without GROMACS all CPUs were loaded on 100%. Here are working files: 1-orca.ZIP

Re: [gmx-users] QM/MM simulations

So, I'v made a little test run based on slightly modified tutorial files. As far as I can judge, mdrun operates properly, ORCA is called and also works OK. Here is zipped working directory. 3.ZIP

Re: [gmx-users] QM/MM simulations

On 4/25/14, 10:58 AM, Iamkaant wrote: Seems that the latest git master + patch combination works. Here is what I did (In order to assure that I did everything properly): 1) Get source code and patch /*git clone https://gerrit.gromacs.org/gromacs* Cloning into 'gromacs'... remote: Counting objec

Re: [gmx-users] QM/MM simulations

Seems that the latest git master + patch combination works. Here is what I did (In order to assure that I did everything properly): 1) Get source code and patch /*git clone https://gerrit.gromacs.org/gromacs* Cloning into 'gromacs'... remote: Counting objects: 163705, done remote: Finding sources:

Re: [gmx-users] QM/MM simulations

On 4/24/14, 12:28 PM, Iamkaant wrote: Thanks for rapid answer! I'm willing to try the latest version with your patch. But since I'm quite new to Linux, I'll be very thankful if you explain me how to use gromacs git server, and apply patches. (where to download the source code and the patch) h

Re: [gmx-users] QM/MM simulations

Thanks for rapid answer! I'm willing to try the latest version with your patch. But since I'm quite new to Linux, I'll be very thankful if you explain me how to use gromacs git server, and apply patches. (where to download the source code and the patch) Sincerely, Andrey. -- View this message in

Re: [gmx-users] QM/MM simulations

On 4/24/14, 9:34 AM, Iamkaant wrote: Dear Justin! I'm very sorry to waste your time, but I've got an issue with ORCA support in GROMACS and hope you can help me. I'm installing gromacs-4.6.5 on my Dell PowerEdge R720 machine running Suse 12.3 x64 ( 3.7.10-1.28-desktop core). Installed version o

Re: [gmx-users] QM/MM simulations

Dear Justin! I'm very sorry to waste your time, but I've got an issue with ORCA support in GROMACS and hope you can help me. I'm installing gromacs-4.6.5 on my Dell PowerEdge R720 machine running Suse 12.3 x64 ( 3.7.10-1.28-desktop core). Installed version of ORCA is orca_3_0_0_linux_x86-64. 0)Prev