Re: [gmx-users] QM/MM simulations

[Clinton King]

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'm trying to
> verify that I'm getting the right information out of Gromacs to send over
> to Gaussian (the input.com file). I might be misreading the "gau" script (
> http://wwwuser.gwdg.de/~ggroenh/gau), but I think it's saying that there
> should be two coordinate sections: the first section should contain the
> cartesian coordinates for the QM atoms, while the second section should
> contain the coordinates for the MM atoms as a field of point charges.
>
> I was attempting to simulate octanol in water solvent. The octanol atoms
> are to be treated by QM. I am pasting the body of the file in below. I can
> see that the MM coordinates were not included in the file. Has anyone seen
> this problem before?
>
> %chk=input
> %mem=1215752192
> %subst l701 /fslhome/crk9/gromacs_src/modlinks/l701
> %subst l301 /fslhome/crk9/gromacs_src/modlinks/l301
> %subst l /fslhome/crk9/gromacs_src/modlinks/l
> #P  DFT/3-21G*
> Nosymm units=bohr
> FORCE Punch=(Derivatives) iop(3/33=1)
>
> input-file generated by gromacs
>
>  0 1
>   1 62.2773850  18.0042321  12.8730289
>   8 62.7275929  19.6615469  13.5481707
>   1 60.8732094  22.8994305  14.4701237
>   1 61.3726754  22.4880551  11.2309538
>   6 60.8813102  21.4923398  12.9658582
>   1 58.3447012  18.6825131  11.6416004
>   1 56.8749667  21.5528031  12.3468668
>   6 58.2902482  20.2147180  13.0171607
>   1 55.7188751  17.8600687  15.1328293
>   1 58.8560031  18.0276177  16.2996878
>   6 57.3035799  19.1226107  15.5035981
>   1 58.1924753  22.3120539  17.8026816
>   1 55.1397300  22.2786189  16.7532522
>   6 56.5899874  21.0450109  17.5392182
>   1 54.3066933  18.3180812  19.3290486
>   1 57.3206195  18.3784025  20.4499142
>   6 55.7745716  19.6343339  19.9253595
>   1 56.0312610  22.6056363  22.6202497
>   1 52.9728344  22.2488265  21.3282668
>   6 54.6149342  21.2279325  22.0382414
>   1 55.1450509  17.9434118  24.4976697
>   1 51.9915096  19.0228103  24.2290069
>   6 53.9589936  19.6208130  24.3481110
>   1 55.7838078  22.2669272  26.6621999
>   1 54.5106599  19.8634027  28.4811908
>   1 52.4125626  22.0430645  27.4308446
>   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,  @maillist.sys.kth.se> wrote:
>
>>
>> Today's Topics:
>>
>>1. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit)
>>   (Clinton King) (Groenhof, Gerrit)
>> ----------
>> ----
>>
>> Message: 1
>> Date: Thu, 1 Sep 2016 10:08:19 +
>> From: "Groenhof, Gerrit" <ggro...@gwdg.de>
>> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>> <gromacs.org_gmx-users@maillist.sys.kth.se>
>> Subject: Re: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
>> Gerrit) (Clinton King)
>> Message-ID:
>> <858a7947bc0fe04da05e1786a6d51d453307f...@um-excdag-a05.um.g
>> wdg.de>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> No, it also works in gmx5.
>>
>> Don't use domain decomposition or the verlet scheme (use group based
>> cut-off instead) and run a single thread (-nt 1)
>>
>>
>> Hope it works of you too,
>>
>> Best,
>>
>> Gerrit
>>
>>
>>
>>
>>
>> --
>>
>> Message: 1
>> Date: Wed, 31 Aug 2016 13:28:56 -0600
>> From: Clinton King <clintonkin...@chem.byu.edu>
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
>> Gerrit)
>> Message-ID:
>> 

Re: [gmx-users] QM/MM simulations

[Clinton King]

I'm still working on the same problem I mentioned below. I'm trying to
verify that I'm getting the right information out of Gromacs to send over
to Gaussian (the input.com file). I might be misreading the "gau" script (
http://wwwuser.gwdg.de/~ggroenh/gau), but I think it's saying that there
should be two coordinate sections: the first section should contain the
cartesian coordinates for the QM atoms, while the second section should
contain the coordinates for the MM atoms as a field of point charges.

I was attempting to simulate octanol in water solvent. The octanol atoms
are to be treated by QM. I am pasting the body of the file in below. I can
see that the MM coordinates were not included in the file. Has anyone seen
this problem before?

%chk=input
%mem=1215752192
%subst l701 /fslhome/crk9/gromacs_src/modlinks/l701
%subst l301 /fslhome/crk9/gromacs_src/modlinks/l301
%subst l /fslhome/crk9/gromacs_src/modlinks/l
#P  DFT/3-21G*
Nosymm units=bohr
FORCE Punch=(Derivatives) iop(3/33=1)

input-file generated by gromacs

 0 1
  1 62.2773850  18.0042321  12.8730289
  8 62.7275929  19.6615469  13.5481707
  1 60.8732094  22.8994305  14.4701237
  1 61.3726754  22.4880551  11.2309538
  6 60.8813102  21.4923398  12.9658582
  1 58.3447012  18.6825131  11.6416004
  1 56.8749667  21.5528031  12.3468668
  6 58.2902482  20.2147180  13.0171607
  1 55.7188751  17.8600687  15.1328293
  1 58.8560031  18.0276177  16.2996878
  6 57.3035799  19.1226107  15.5035981
  1 58.1924753  22.3120539  17.8026816
  1 55.1397300  22.2786189  16.7532522
  6 56.5899874  21.0450109  17.5392182
  1 54.3066933  18.3180812  19.3290486
  1 57.3206195  18.3784025  20.4499142
  6 55.7745716  19.6343339  19.9253595
  1 56.0312610  22.6056363  22.6202497
  1 52.9728344  22.2488265  21.3282668
  6 54.6149342  21.2279325  22.0382414
  1 55.1450509  17.9434118  24.4976697
  1 51.9915096  19.0228103  24.2290069
  6 53.9589936  19.6208130  24.3481110
  1 55.7838078  22.2669272  26.6621999
  1 54.5106599  19.8634027  28.4811908
  1 52.4125626  22.0430645  27.4308446
  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, Gerrit)
>   (Clinton King) (Groenhof, Gerrit)
> --
>
> Message: 1
> Date: Thu, 1 Sep 2016 10:08:19 +
> From: "Groenhof, Gerrit" <ggro...@gwdg.de>
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
>     <gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: Re: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
> Gerrit) (Clinton King)
> Message-ID:
> <858a7947bc0fe04da05e1786a6d51d453307f...@um-excdag-a05.um.gwdg.de
> >
> Content-Type: text/plain; charset="us-ascii"
>
> No, it also works in gmx5.
>
> Don't use domain decomposition or the verlet scheme (use group based
> cut-off instead) and run a single thread (-nt 1)
>
>
> Hope it works of you too,
>
> Best,
>
> Gerrit
>
>
>
>
>
> --
>
> Message: 1
> Date: Wed, 31 Aug 2016 13:28:56 -0600
> From: Clinton King <clintonkin...@chem.byu.edu>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
> Gerrit)
> Message-ID:
> 

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

[Groenhof, Gerrit]

No, it also works in gmx5.

Don't use domain decomposition or the verlet scheme (use group based cut-off 
instead) and run a single thread (-nt 1)


Hope it works of you too,

Best,

Gerrit





--

Message: 1
Date: Wed, 31 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:

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

[Groenhof, Gerrit]

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 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 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
> communicated correctly, ie the output looks like the following:
>
>
>
>Step   Time Lambda
>70007.00.0
>
>Energies (kJ/mol)
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>  Quantum En.
> 2.45033e+04   -1.74106e+02   -1.86935e+056.68753e+010.0e+00
>   Potential  Kinetic En. Total EnergyTemperature
>  Pres. DC (bar)
>-1.62539e+053.00966e+04   -1.32443e+052.97582e+02   -2.34549e+01
>  Pressure (bar)   Constr. rmsd
>-7.37300e+018.07450e-06
>
>
> Notice that the 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] QM/MM simulations

[Mark Abraham]

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 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
> communicated correctly, ie the output looks like the following:
>
>
>
>Step   Time Lambda
>70007.00.0
>
>Energies (kJ/mol)
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>  Quantum En.
> 2.45033e+04   -1.74106e+02   -1.86935e+056.68753e+010.0e+00
>   Potential  Kinetic En. Total EnergyTemperature
>  Pres. DC (bar)
>-1.62539e+053.00966e+04   -1.32443e+052.97582e+02   -2.34549e+01
>  Pressure (bar)   Constr. rmsd
>-7.37300e+018.07450e-06
>
>
> Notice that the 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
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Re: [gmx-users] QM/MM simulations

[Justin Lemkul]

On 4/29/14, 4:46 AM, Iamkaant wrote:

So, I'v made a little test run based on slightly modified  tutorial
http://wwwuser.gwdg.de/~ggroenh/EMBO2004/html/qmmmvacuum.html#top  files.
As far as I can judge, mdrun operates properly, ORCA is called and also
works OK.
Here is zipped working directory.  3.ZIP
http://gromacs.5086.x6.nabble.com/file/n5016133/3.ZIP
One thing that bothers me is sluggishness of ORCA optimization steps -- they
took probably 99.9% of wall-time. Earlier I'v made optimizations by this
instance of ORCA and they went very fast, so the issue may be in the input
parameters. But since I'm not very familiar with it, I can't say what slows
down calculation for system of less than 30 atoms at RHF/3-21G level.


IIRC, that is to be expected.  mdrun simply serves as a wrapper to pass 
information back and forth with ORCA, and the QM part of the calculation in 
Gromacs QM/MM can only be executed in serial, so it will be very slow.


Thanks for reporting back; it's good to know that things are working (even if 
performance could stand to be improved).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] QM/MM simulations

[Iamkaant]

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)Previos steps according to the  installation guide
http://www.gromacs.org/Documentation/Installation_Instructions  .
1) cmake
/*cmake .. -DGMX_MPI=ON -DGMX_QMMM_PROGRAM=ORCA
-DCMAKE_INSTALL_PREFIX=/opt/GROMACS-ORCA/ -DGMX_DOUBLE=on
-DFFTW_LIBRARY=/usr/lib64/libfftw3.so.3*/

I get following output. CMake-output.txt
http://gromacs.5086.x6.nabble.com/file/n5016041/CMake-output.txt  
Contents of CMakeCache file is here.  CMakeCache.txt
http://gromacs.5086.x6.nabble.com/file/n5016041/CMakeCache.txt  
The GMX_QMMM_PROGRAM variable is properly set in CMakeCache.txt:

/*# grep GMX_QMMM_PROGRAM CMakeCache.txt *
GMX_QMMM_PROGRAM:STRING=ORCA 
//ADVANCED property for variable: GMX_QMMM_PROGRAM
 GMX_QMMM_PROGRAM-ADVANCED:INTERNAL=0/ 

and in src/config.h

/*# grep #define GMX_QMMM_ORCA src/config.h *
#define GMX_QMMM_ORCA/

2) make  make install, everything without errors.
3) I create .mdp-file with following QMMM parameters

/QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = 3-21G
QMMMscheme   = normal
QMcharge = 0
QMmult   = 1/

and  .ORCAINFO file (as stated in ORCA manual)

/# Optimization step in the Lennard-Jones and point charges field of the MM
atoms
! QMMMOpt
# file containing the Lennard Jones coefficients for the Lennard-Jones
interaction
#%LJCoefficients temp.LJ
# file containing the point charges for the electrostatic interaction
#%pointcharges temp.pc
%geom
# calculate the exact Hessian before the first optimization step
Calc_Hess true
# in case of a TS optimization the updated Hessian of the previous
# TS optimization run is read instead of calculating a new one
read_temp_Hess true
end/

Variables are set as follows: $BASENAME=topol (name of .tpr and .ORCAINFO
files) and  $ORCA_PATH=/opt/orca_3_0_0_linux_x86-64
I run
//*opt/GROMACS-ORCA/bin/mdrun_mpi_d -v*/
and get 

/...
Back Off! I just backed up md.log to ./#md.log.8#
Reading file topol.tpr, VERSION 4.6.5 (double precision)
Using 1 MPI process
QM/MM calculation requested.
Layer 0
nr of QM atoms 24
QMlevel: RHF/3-21G
---
Program mdrun_mpi_d, VERSION 4.6.5
Source code file: /home/ak87/Downloads/gromacs-4.6.5/src/mdlib/qmmm.c, line:
778
Fatal error:
Ab-initio calculation only supported with Gamess, Gaussian or ORCA.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Halting program mdrun_mpi_d
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--/

It is quite strange since such problem was noted in earlier versions of
GROMACS and have been solved by your patch. Therefore, it should not arise
in version 4.6.5, particularly because all variables connected to ORCA are
properly defined in Cmake config files.
Hope for hearing from you. Thanks in advance! 
Sincerely yours,
Andrey.


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Re: [gmx-users] QM/MM simulations

[Iamkaant]

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.


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Re: [gmx-users] QM/MM simulations

[Justin Lemkul]

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)


http://www.gromacs.org/Developer_Zone/Git#Checking_out_the_Gromacs_source_code_using_git

Then use the magic copy-paste command that Gerrit gives you (the Download box 
in checkout mode) on https://gerrit.gromacs.org/#/c/3395/ to apply the patch.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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