On Thu, Jan 01, 2015, newamber list wrote:
>
> 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?
Yes.
>
> 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
> acceptable?
>
It's not clear what you mean by "different temperature controls". Diffusion
constants are strongly dependent upon temperature, and also upon the force
field. (In particular, TIP3P water is dramatically different from most other
popular water models; this may also influence ionic diffusion.
Be sure that you are not just looking at anectodal evidence. You mention
"ions in some constricted space": if there are not very many of these, you
may have considerably difficulty in getting a converged result.
....dac
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Received on Fri Jan 02 2015 - 05:30:03 PST
