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
>
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Sep 06 2016 - 08:30:02 PDT
