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 .
Regards
Tanmoy
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 18 2014 - 00:00:02 PDT
