Dear Prof David and Gerald,
Thanks for your replies and explanations, those are helpful. The problem is
solved by cleaning the directory and re-running the optimization.
Regards
Kshatresh
On Fri, Jun 13, 2014 at 10:39 PM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:
> Hi,
>
> In addition to Dave's reply, the 'OPT' keyword that you include in your
> template is overridden by the 'Force' keyword that is added by sander.
> This keyword asks Gaussian to compute only the energy and the forces
> (=minus the gradient). That's all. That's why you see a huge difference
> in timings and outputs between keeping or manually removing the 'Force'
> keyword.
> Don't forget that, you are asking a QM/MM calculation, that means you
> need to compute the energy of the MM part (done by sander), the QM part
> (done by Gaussian), and the interaction between the QM and the MM part
> (done partially by sander and partially by Gaussian). You cannot have
> the two programs to change the system coordinates independently!
> Therefore, only one program should handle the optimization (and,
> therefore, take care of modifying the coordinates of every atoms).
> In other (now politically incorrect?) words, let's say that in Amber,
> sander is the "master" program and Gaussian, and by extension all EXTERN
> programs, are "slave" programs. Only the master program has the right to
> modify the coordinates, here either for minimization or molecular dynamics.
>
> Gerald.
>
> On 06/13/2014 04:58 PM, Kshatresh Dutta Dubey wrote:
> > Dear Prof Monard,
> > Thanks for your detailed explanation, it is really helpful. However,
> I
> > have still some queries. QM/MM run using Gaussian is producing some file,
> > like old.gau_job.log, old.gau_job.inp and others. When I am checking
> > *old.gau_job.log
> > *file there is no proper convergence informations as usually we find in
> any
> > Gaussian optimized output file. Indeed it successfully finishes proper
> > termination in less than 1 hour while number of atoms are more than 100.
> > When I ran same old.gau_job.inp file by remove 'Force' keyword appended
> by
> > sander, it runs as usual QM optimizations and prints all convergence
> > informations and takes relatively very long time in proper convergence (
> > same input without 'Force' keyword on same machine). Therefore, I guess
> > that even assigning min=1 keyword, Gaussian is not optimizing the system
> > and only computing its energy (as single point calculations).
> > I am attaching old.gau_job.inp as well as QM-MM.in. I request you to
> > tell me where am I doing a mistake. I will be thankful for your help.
> >
> > With Regards
> > Kshatresh
> >
> >
> >
> > On Fri, Jun 13, 2014 at 4:48 PM, Gerald Monard <
> > Gerald.Monard.univ-lorraine.fr> wrote:
> >
> >> Hi,
> >>
> >> On 06/13/2014 01:26 PM, Kshatresh Dutta Dubey wrote:
> >>> Dear Jason,
> >>>
> >>> I am looking for QM optimization, I know that using imin=1 will
> >> give me
> >>> minimized structure but I think that it will molecular mechanically
> >>> minimize the system, but what for QM optimizations?
> >>
> >> No. imin=1 will minimize the _whole_ system: QM _+_ MM, except if you
> >> use some kind of restraints (ibelly, which is not recommended for
> >> minimization).
> >> Minimization means "energy minimization": you compute the energy of the
> >> _whole_ system (QM + MM and their interactions), the gradient, and from
> >> the latter, the minimization algorithm decide how to modify the
> >> coordinates of the whole system to obtain a new set of coordinates that
> >> should lead to a lower energy.
> >> That is to say: to perform minimization, the algorithm must have
> >> information on the whole system, not part of it.
> >>
> >> If you refer to some kind of minimization algorithm as develop in the
> >> group of Weitao Yang some years ago or in the group of Keiji Morokuma
> >> (iterative minimization, J. Chem. Phys. 112, 3483--3492 (2000) or J.
> >> Comp. Chem., 24, 760-769 (2003)), this is not implemented in Amber.
> >>
> >>
> >>> If I have to use
> >>> sander for minimization then what is the use of implementation of
> >> Gaussian
> >>> interface? I am curious to know that - is it possible to perform QM
> >>> optimization of QM region using external QM program and sander for MM
> >>> region. If yes then what should I do? Using following input (complete
> >>> input, I used) does not optimize the QM region, it does single point
> >> energy
> >>> calculations only, while sander does optimize MM region.
> >>
> >> In the input below, both regions are optimized at the same time (as
> >> there is only 1 energy computed: a QM/MM energy).
> >>
> >> Gerald.
> >>
> >>
> >>>
> >>> *QM-MM calculations for FMN domain *
> >>> *&cntrl*
> >>> * imin=1, maxcyc=10,*
> >>> * ntb=0,*
> >>> * cut=20.,*
> >>> * ifqnt=1*
> >>> * /*
> >>> * &qmmm*
> >>> * qmmask ='.819-830,2244-2295',*
> >>> * qmcharge=0,*
> >>> * spin =1,*
> >>> * qm_theory='EXTERN',*
> >>> * qmcut=20.0*
> >>> * /*
> >>> * &gau*
> >>> * mem = '2GB'*
> >>> *! method = 'B3LYP',*
> >>> *! basis = '6-31G',*
> >>> * use_template =1,*
> >>> * num_threads = 2*
> >>> * /*
> >>>
> >>> Thanks and regards
> >>> Kshatresh
> >>>
> >>>
> >>>
> >>> On Fri, Jun 13, 2014 at 2:01 PM, Soumendranath Bhakat <
> >>> bhakatsoumendranath.gmail.com> wrote:
> >>>
> >>>> Use these input for minimization if you are using QM/MM. Please use
> >> sander
> >>>> and sander.MPI for running
> >>>>
> >>>> Full_Mini.in
> >>>>
> >>>> Initial minimization of QMMM: solvent molecules and added ions
> >>>> &cntrl
> >>>> imin = 1,
> >>>> maxcyc = 2500,
> >>>> ncyc = 750,
> >>>> ntb = 1,
> >>>> ntr = 1,
> >>>> cut = 12.0,
> >>>> ifqnt = 1,
> >>>> /
> >>>> &qmmm
> >>>> qmmask= '557,250,238.75,86,89,75',
> >>>> qmcharge=0,
> >>>> qmtheory=7, *(please suggest check once)*
> >>>> qmshake=1,
> >>>> qm_ewald=1,
> >>>> qm_pme=1,
> >>>> /
> >>>>
> >>>> Hold the Protein fixed
> >>>> 10.0
> >>>> RES 1 557
> >>>>
> >>>> All the best.
> >>>>
> >>>>
> >>>> On Fri, Jun 13, 2014 at 12:54 PM, Jason Swails <
> jason.swails.gmail.com>
> >>>> wrote:
> >>>>
> >>>>>
> >>>>>
> >>>>>> On Jun 13, 2014, at 5:50 AM, Kshatresh Dutta Dubey <
> >>>> kshatresh.gmail.com>
> >>>>> wrote:
> >>>>>>
> >>>>>> Dear Prof Monard,
> >>>>>>
> >>>>>> Many thanks for your quick response, still I am unable to find
> any
> >>>>>> keyword that handles the optimizing process in sander. I went
> through
> >>>> the
> >>>>>> manual bt I was unable to find such keyword. I will deeply
> appreciate
> >>>> you
> >>>>>> if you help me to handle this process so that I can get proper QM
> >>>>>> optimization.
> >>>>>> Thanking you again.
> >>>>>
> >>>>> What you're looking for is a basic minimization. Look at the imin and
> >>>>> ntmin flags.
> >>>>>
> >>>>> HTH,
> >>>>> Jason
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> On Fri, Jun 13, 2014 at 12:31 PM, Gerald Monard <
> >>>>>> Gerald.Monard.univ-lorraine.fr> wrote:
> >>>>>>
> >>>>>>> Hi,
> >>>>>>>
> >>>>>>> You cannot use the Gaussian optimizer since it is sander that
> masters
> >>>>>>> what happens to the coordinates (from a coordinate set, sander asks
> >>>>>>> gaussian to compute an energy, it does not let gaussian modify
> them,
> >>>>>>> hence the "force" keyword).
> >>>>>>> You'd better use one of the optimizers available in sander (&cntrl
> >>>>>>> namelist) instead.
> >>>>>>>
> >>>>>>> Gerald.
> >>>>>>>
> >>>>>>>
> >>>>>>>> On 06/13/2014 11:16 AM, Kshatresh Dutta Dubey wrote:
> >>>>>>>> Dear Users
> >>>>>>>>
> >>>>>>>> I am using Amber 14 for QM/MM calculation with Gaussian as
> >>>> external
> >>>>>>>> interface. I have to optimize a system containing some amino acids
> >>>> and
> >>>>> a
> >>>>>>>> ligand in QM regions. I found that Amber automatically adds some
> >>>>> keywords
> >>>>>>>> in route section of Gaussian input that force Gaussian to do
> single
> >>>>> point
> >>>>>>>> calculations. For example, I used :
> >>>>>>>> *&gau*
> >>>>>>>> * mem = '2GB'*
> >>>>>>>> *! method = 'B3LYP',*
> >>>>>>>> *! basis = '6-31G',*
> >>>>>>>> * use_template =1,*
> >>>>>>>> * num_threads = 2*
> >>>>>>>> * /*
> >>>>>>>> for &gau namelist and :
> >>>>>>>>
> >>>>>>>> *#P OPT B3LYP/6-31G SCF=(Conver=8)*
> >>>>>>>>
> >>>>>>>> for template file namelist. The calculations runs fine and it
> shows
> >>>>>>> normal
> >>>>>>>> termination, but I found that it does only single point
> calculation
> >>>> not
> >>>>>>>> optimizing the structure while I have mentioned optimization in
> >> route
> >>>>>>>> sections. I notice that Amber adds some additional keyword such as
> >>>>>>> 'Force'
> >>>>>>>> in route section which restricts Gaussian to calculate forces
> only.
> >> I
> >>>>>>> guess
> >>>>>>>> it is fine for QM-MM/MD since we need forces for dynamics, but
> here
> >> I
> >>>>> am
> >>>>>>>> interested in QM/MM optimization only. The route section modified
> by
> >>>>>>> Amber
> >>>>>>>> is :
> >>>>>>>>
> >>>>>>>> *#P OPT B3LYP/6-31G SCF=(Conver=8) NoSymm Force Guess=Read Charge
> >>>>> Prop=*
> >>>>>>>> * (Field,Read)*
> >>>>>>>>
> >>>>>>>> How can I disable 'Force' keyword so that I can perform proper
> >>>>>>>> optimization. I will be thankful for your help.
> >>>>>>>>
> >>>>>>>> thanks
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>>>
> >>>>>
> >>>>
> >>
> ____________________________________________________________________________
> >>>>>>>
> >>>>>>> Prof. Gerald MONARD
> >>>>>>> SRSMC, Université de Lorraine, CNRS
> >>>>>>> Boulevard des Aiguillettes B.P. 70239
> >>>>>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
> >>>>>>>
> >>>>>>> e-mail : Gerald.Monard.univ-lorraine.fr
> >>>>>>> tel. : +33 (0)383.684.381
> >>>>>>> fax : +33 (0)383.684.371
> >>>>>>> web : http://www.monard.info
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>
> >>>>
> >>
> ____________________________________________________________________________
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> AMBER mailing list
> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> With best regards
> >>>>>>
> >>>>>
> >>>>
> >>
> ************************************************************************************************
> >>>>>> Dr. Kshatresh Dutta Dubey
> >>>>>> Post Doctoral Researcher,
> >>>>>> c/o Prof Sason Shaik,
> >>>>>> Hebrew University of Jerusalem, Israel
> >>>>>> Jerusalem, Israel
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>> --
> >>>>> Jason M. Swails
> >>>>> BioMaPS,
> >>>>> Rutgers University
> >>>>> Postdoctoral Researcher
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Thanks & Regards;
> >>>> Soumendranath Bhakat
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>
> >> --
> >>
> >>
> ____________________________________________________________________________
> >>
> >> Prof. Gerald MONARD
> >> SRSMC, Université de Lorraine, CNRS
> >> Boulevard des Aiguillettes B.P. 70239
> >> F-54506 Vandoeuvre-les-Nancy, FRANCE
> >>
> >> e-mail : Gerald.Monard.univ-lorraine.fr
> >> tel. : +33 (0)383.684.381
> >> fax : +33 (0)383.684.371
> >> web : http://www.monard.info
> >>
> >>
> >>
> ____________________________________________________________________________
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
>
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
>
> ____________________________________________________________________________
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
************************************************************************************************
Dr. Kshatresh Dutta Dubey
Post Doctoral Researcher,
c/o Prof Sason Shaik,
Hebrew University of Jerusalem, Israel
Jerusalem, Israel
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Received on Fri Jun 13 2014 - 14:30:02 PDT
