[gmx-users] Gromacs2019 + Gaussian09 QMMM (nikolaev at spbau.ru)

[Groenhof, Gerrit]

Hi

Good point. The environment variable names changed.

Thus 

$GMX_QM_MODIFIED_LINKS_DIR  is what used to be DEVIL_DIR

The same for the others.

Gerrit


> Good  4. Re: Gromacs2019 + Gaussian09 QMMM (nikolaev at spbau.ru)
>   
> 
> Dear Gerrit,
> 
> Thank you very much for your answer.
> As I understand, I do not to modify links if I use gau script.
> I have put the gau script (with all necessary modifications) into folder
> ~/test/gau
> export GAUSS_DIR=~/test/gau
> export GAUSS_EXE=gau
> Created the empty directory ~/test/devil
> export DEVIL_DIR=~/test/devil
> 
> However, mdrun still fails with the following error:
> 
> Fatal error:
> no $GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside.
> 
> 
> What am I doing wrong?
> 
> Best,
> Dmitrii
> 
> 
> 
> 
> 
> 
>> 
>> Dear Dmitrii,
>> 
>> Unfortunately, the group nb-search scheme that was needed for QM/MM is
>> discontinued. Because it still worked in the 2018 version, I suggest that
>> you use the previous version until the problem is fixed.
>> 
>> Use
>> -DGMX_QMMM_PROGRAM=gaussian
>> in the cmake command to compile with support. Details on how to link
>> gaussian09 can be found here:
>> http://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian
>> It probably is easiest to use the gau script to make the two programs talk
>> to each other.
>> 
>> Good luck,
>> 
>> Gerrit
>> 
>> 
>> 
>> ________________________________
>> 
>> 
>> Dear all,
>> 
>> I am planning to run QM/MM dynamics (ONIOM), following the approach
>> described here
>> http://manual.gromacs.org/2019/reference-manual/special/qmmm.html#output
>> 
>> (not the MiMiC, because it has only an additive scheme), Gaussian09 as the
>> QM package.
>> 
>> However, I could not find any information on compilation of gromacs 2019
>> with Gaussian, only CP2K for MiMiC support:
>> 
>> http://manual.gromacs.org/documentation/2019/install-guide/index.html
>> 
>> Where I can find the information on the Gromacs2019+Gaussian09 QMMM
>> installation?
>> 
>> Best,
>> Dmitrii
>> 
>> 
>> 
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> 
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Sat, 5 Oct 2019 23:28:55 +0530
> From: Quin K <profiles.ke at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] RMSD analysis of protein-ligand complex
> Message-ID:
> 	<CAG0e8MMjQPR=RwrB5D5bEsyvbNABqywLtBsuTFbkMoFM-FUFZA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
> 
> Thank you.
> 
> I examined the trajectory using VMD and noted that ligand had come out of
> the binding site and is running around.
> How is this possible? I have used the guidelines in mdtutorials.com to set
> up the system.
> However it's worth noting that there was a power failure around the same
> time (23ns) and I had to restart MD with append command.
> Could this have had an affect on MD? Do I have to recreate trajectory file
> after restarting MD, instead of using the default trajectory?
> 
> Regards
> 
> On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 
>> 
>> 
>> On 10/5/19 11:59 AM, Quin K wrote:
>>> Thank you.
>>> 
>>> I got following when I analysed Ligand RMSD protein backbone as east
>> square
>>> fit.
>>> Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7>
>>> Can you please comment why there's high fluctuation after like 23 ns?
>>> What could this mean?
>> 
>> Watch the trajectory and see what is going on. Make sure you've properly
>> re-imaged to account for PBC effects.
>> 
>> -Justin
>> 
>> --
>> ==================================================
>> 
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>> 
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> 
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>> 
>> ==================================================
>> 
>> --
>> Gromacs Users mailing list
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> 
> 
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