Re: [AMBER] diffusion time step

From: newamber list <>
Date: Fri, 2 Jan 2015 16:12:07 +0000

Dear David,

Thanks for your reply.

>> It's not clear what you mean by "different temperature controls"

Sorry I used the term lightly. AMBER one is with Berendsen and CHARMM with
langevin dynamics.

>> You mention "ions in some constricted space": if there are not very many
of these, you may have considerably difficulty in getting a converged

Yes that is true. For my one case (AMBER) coordinates are saved after 2 ps
and in this constricted volume I actually take an average over long part of
simulation and over all the particles. I get quite linear MSD vs time
relation upto 12-14 ps (linear line with 6 points) from which I get
diffusion coefficient values. Hope its fine?

But in CHARMM case, someone can suggest, I have frames saved after 10 ps
only. So problem is having less samples of particles in constricted space
(volume) which is not reliable. Other thing is in 10 ps a particle may
leave and enter the same volume that will be counted as regular path which
is wrong (single event). As particle can come inside, stay and then leave
small volume few times in 10 ps those should be counted as different
events. Also the particle may stay in constricted space for long (~20-30
ps) then in this case am averaging over only slow diffusing particles hence
may be am getting three times lower values than AMBER case in which I can
capture both fast and slow particles as frames are saved after 2ps. I am
not sure if am thinking correctly.

 Indeed it should not matter if we take 2ps or 10 ps time step for
diffusion calculation if it was done on infinite bulk volume without any

Thanks for your time and suggestions.


On Fri, Jan 2, 2015 at 1:10 PM, David A Case <>

> 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 - 08:30:03 PST
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