[AMBER] diffusion time step

From: newamber list <newamberlist.gmail.com>
Date: Thu, 1 Jan 2015 02:14:59 +0000

Dear All,

I have question related to diffusion time step that we define in cpptraj
'diffusion' calculation. Query divided in two parts:

1) I have trajectory coordinates saved after 2ps, thus in cpptraj I will
define time_per_frame as 2. But if same trajectory is used with frames
stripped and saved after 10 ps and using time_per_frame as 10 then should I
expect nearly same diffusion coeff. values?

2) Actually I have some complex situation and I have number of variables. I
have one simulation with AMBER ff and other with CHARMM and time frames
saved after 2 and 10 ps respectively that too with different temperature
controls. I am getting three times difference in the diffusion values for
ions in some constricted space of interest. I am not sure whether I should
expect the differences or not. If yes then such (three times) difference is

Please suggest.

Thanks for any suggestion
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Received on Wed Dec 31 2014 - 18:30:02 PST
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