back-to-back repetition of Hamiltonian for longer NAMD calculations?

[Hamid Mehdipour]

Dear Pyxaid users and developers

I am wondering how one can repeat single Hamiltonian for a short period of time (e.g., 3 ps) to do NAMD calculation for longer times ( 6 to 15 ps time periods, for example).

How one can take a final state of quantum system (at the end of 3 ps time period) and use it as initial states for the repetition? how can this be resolve using in input pyxaid file?

Looking forward to hearing your points/response

Thanks

Hamid

[Alexey Akimov]

Hi Hamid,

The easiest way is to copy existing files into new files. E.g. say you have files Ham_0, Ham_1, ... Ham_999 (1 ps trajectory). 

Then if you copy files like Ham_0 --> Ham_1000, Ham_1 --> Ham_1001, .... Ham_999 --> Ham_1999, you have a 2 ps trajectory.

Having said that I don't know if that iteration is well justified. One apparent problem is that why should we continue like that, and not, say, in the opposite direction that is:

Ham_0 --> Ham_1999, Ham_1 --> Ham_1998, .... Ham_999 --> Ham_1001 ?

Perhaps, someone could investigate this problem. 

But, in any case, I hope this should help you to do what you want.

Best,

Alexey

[Hamid Mehdipour]

Hi Alexey,

Many thanks for your prompt reply.. Hope that the method helps.

Best

Hamid