Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj

From: Daniel Roe via AMBER <>
Date: Tue, 6 Sep 2022 10:45:43 -0400


On Fri, Sep 2, 2022 at 12:51 PM Cianna Calia <> wrote:
> That does make sense, thanks a lot for the explanation!
> But then this confuses me with regard to how to correctly do the type of analysis I was trying - I'm attempting to get MSD values from water Os near different residues of my protein (see left column of pg. 17894 of this paper if more detail is useful). To assess water diffusion with respect to the protein, it seems to me like the protein would need to be held still, either via some post-processing of the trajectory or by using a simulation where the backbone was restrained... Am I thinking along the right lines here?

In that case you should probably try the 'stfcdiffusion' command which
is a diffusion calculation written by Hannes Loeffler from STFC
Daresbury, in which you can supply a second mask (via 'mask2 <mask2>')
and an upper and lower bounds (via 'upper <upper>' and 'lower
<lower>') to calculate diffusion within a region from <mask2> bounded
by <lower> and <upper> (see the manual for full details). This is
functionality I'd like to eventually merge into 'diffusion' but just
haven't had the time. I don't think that command takes imaging into
account, so you'll want to image beforehand. As long as the regions
don't cross the unit cell boundary this should be fine. Hope this


> Many thanks,
> Cianna
> On Fri, Sep 2, 2022 at 5:08 AM Daniel Roe <> wrote:
>> Hi Cianna,
>> On Fri, Sep 2, 2022 at 12:08 AM Cianna Calia <> wrote:
>> >
>> > Hi Dan - I've been trying some more tests with your diffusion function, and I notice that the MSD values are different if I recenter my trajectory with autoimage. I'm not sure why that would be... Is this expected? Any clarification on why this happens would be appreciated - more details below:
>> Yes, this is expected. The 'autoimage' command centers the system on
>> the anchor in addition to imaging, so there is an applied translation
>> that is effectively removing the global translation of the anchor from
>> the entire system, which is why the diffusion calculation is affected.
>> If you just use 'image' (which does not automatically apply a
>> translation) instead of 'autoimage' the calculation should be
>> unaffected. Does that make sense? Let me know if not.
>> -Dan

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Received on Tue Sep 06 2022 - 08:00:02 PDT
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