VMD-L Mailing List

From: sarah k (dailycolors_at_gmail.com)
Date: Sun Jun 12 2011 - 05:57:46 CDT

Dear Axel and Hamzeh,

Thanks for your replies. We have put our protein in nitrogen drift gas,
experimentally and now we need to simulate it.

 how high of a pressure of nitrogen do you expect to model?
>

*P=* 1 atm

> how is the nitrogen supposed to impact the protein, if at all?
>

 The protein is ionizined by high voltage in the drift gas.

> technically, it is of course possible, but before you do this,
> please do a back of the envelope calculation:
> - assume the nitrogen is an ideal gas
> - the desired pressure and volume of your gas box
> - calculate how many nitrogen atoms would be in that box
>

*N=* 10^28 molecules, T= 438 K, V= 0.085 L

The final result may differ signiciently if I suppose the protein in water
or vacuum.

Regards,
F. Keshavarz