[AMBER] Queries about QM/MM

From: Tanmoy Paul <tanmoy635.gmail.com>
Date: Wed, 18 Jun 2014 12:06:51 +0530

Dear amber users,
                             Sorry to disturb you again. I need some
clarifications about qm/mm. All my jobs are running quite well . There is
no problem with that . But the point is while running these simulations in
amber I just have to specify the QM -zone and that's it . I don't have any
control over my simulation as I am relying on some parameters for each
atoms downloaded from the DFTB -website and hopping that everything will go
fine .
I have run the simulations for quite a long time but it seems nothing is
happening . Now my questions are........

1) How the program recognize the atoms which are supposed to take part in
the reaction ( because there are lots of other atoms in the qm -zone) ?

2) Is there any average time limit for any reaction to occur ( like in my
case the proton transfer ) because it will give me some idea about how long
I have to continue ?

3) Can I see the reaction happening in VMD ?

4) What is the time scale for a reaction to happen ( is it in atosec or
femtosec time scale?) ?

5) Can I do something more meaningful than just waiting for this reaction
to happen ?

Sorry for asking so many questions .

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Received on Wed Jun 18 2014 - 00:00:02 PDT
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