Hi Adrian
Thank you for your answer.
I would take your suggestions into account.
All the best !
Anna
________________________________
De: Adrian Roitberg <roitberg.ufl.edu>
Enviat el: dimarts, 6 de setembre de 2016 17:36:18
Per a: AMBER Mailing List
Tema: Re: [AMBER] Question about QM/MM
Hi Anna
A couple of things. The definition of 'active region' is of course
arbitrary, it is up to you to figure out what that means, and if it even
makes sense to define it.
As for the cost of moving all atoms instead of just some, the cost in
terms of a single displacement is almost identical, given that you will
be using a high level of QM theory with an external program. Trying to
minimize water molecules is always a problem, both for MM and QM
methods. Their degrees of freedom are very shallow, so they can move
easily when minimizing.
There are some ways to do what you want to do, but they are VERY picky
to carry out and require lots of tests. I suggest you do not try them
with your level of theory to start with. Try AM1 or something like that,
until you convince yourself that you got the 'right' syntax.
I am not sure if anyone else can share input files, but usually, what
you need is a clever combination of ibelly with bellymask, to tell amber
to only move atoms within certain distance of your QM region.
This is an example of something I tried recently. It uses the xmin
minimizer, which is more efficient than the regular ones.
It is 'supposed' to move ONLY atoms belonging to residues that are
within 10 angstroms of the QM region.
Adrian
restrained minimization
&cntrl
imin=1,maxcyc=1000,ntb=1, cut=10.0
ntmin=3,ncyc=50, drms=1E-05,
ntpr=1,ntwr=10,
ifqnt=1, ntf=1, ntc=1, ioutfm=1,
ibelly=1, bellymask='(:420 | .6361-6372,6430-6451)<:10.0',
&end
&qmmm
qmmask='(:420 | .6361-6372,6430-6451)',
qmcharge=-2,
qm_theory='PM6',
qmshake=0, qm_ewald=1, qm_pme=1, writepdb=0,
qmcut=12.,
&end
&lmod
xmin_verbosity=0,
xmin_method='TNCG',
&end
On 9/6/16 9:26 AM, Anna Cebrian Prats wrote:
> Hi adrian
>
>
> I would like to not move all due to I have 80.000 atoms aprox with the solvent.
>
> So, I would like to move only 2.000 or 3.000 atoms ( active region) and keep frozen the rest.
>
>
> Anna
>
> ________________________________
> De: Adrian Roitberg <roitberg.ufl.edu>
> Enviat el: dimarts, 6 de setembre de 2016 16:44:25
> Per a: AMBER Mailing List
> Tema: Re: [AMBER] Question about QM/MM
>
> Hi Anna
>
> ALL atoms move, all the QM one s and ALL the MM ones.
>
> Why would they not all move? You are trying to optimize the total
> energy, which means every component of the force, for every atom should,
> optimally, go to zero.
>
> Adrian
>
>
>
> On 9/6/16 6:57 AM, Anna Cebrian Prats wrote:
>> Hi dac,
>>
>>
>> Thank you very much for your answer.
>>
>>
>> I already test it and everything is okey. The problem was the rst file of my system.
>>
>>
>> Anyway I already solve this problem and the calculation starts to run.
>>
>> I am waiting for the results or if there are another problem.
>>
>>
>> I would like to ask, why the minimization QMMM input doesn't have any keyword to define which is the active region (= the atoms of the system that moves along the optimization processes)
>>
>>
>> How amber defines the active region? Does the qmcut defines this region or only specifies the size of the electrostátic interactions for QMMM?
>>
>>
>> To sum up, the qmcut is centers on each QM atom or takes all the QM atoms as center?
>>
>>
>> Thank you very much for your help
>>
>>
>> Anna
>>
>> ________________________________
>> De: David A Case <david.case.rutgers.edu>
>> Enviat el: dimarts, 6 de setembre de 2016 13:17:09
>> Per a: AMBER Mailing List
>> Tema: Re: [AMBER] Question about QM/MM
>>
>> On Mon, Sep 05, 2016, Anna Cebrian Prats wrote:
>>> I already prepared the system, but when I tried to run the QM/MM
>>> minimization, the calculation stops here :
>>>
>>> getting new box info from bottom of inpcrd
>>> | INFO: Old style inpcrd file read
>>>
>>> peek_ewald_inpcrd: SHOULD NOT BE HERE ?¿
>>> 91.1230 101.2050 87.7350 90.0000 90.0000 90.0000" Appear at the end of the rst file
>> Does this job run OK if you set ifqnt=0? I suspect that it has nothing
>> to do with QM/MM, but you should run this test to find out. We are probably
>> going to need more information about how you prepared the system.
>>
>> ....dac
>>
>>
>> _______________________________________________
>> 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
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> 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
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
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
Received on Wed Sep 07 2016 - 08:00:02 PDT
