Hi,
I'm pretty sure 'vector minimage' just gives whatever the minimum
imaged vector is - it might be in a neighboring cell or it might not.
You can verify this yourself by ensuring the vector magnitude matches
what you get from 'distance', e.g.
vector v12 minimage ^1 :385 magnitude out vtest.dat.12
distance d12 ^1 :385 out dtest.dat.12
In the above case, the magnitude column of the output from vector
(last column) should match the distance printed to dtest.dat.12 (also
last column).
-Dan
On Thu, Mar 9, 2023 at 2:42 PM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
>
> Hi Dan,
>
>
>
> That’s not quite want I wanted. The output is of the desired format, but doesn’t “vector minimage” compute the center-of-mass distance between mask1 in one unit cell to mask2 in the adjacent unit cell? I need the vector components of the minimum distance between mask1 and mask2 in the same unit cell.
>
>
>
> Best,
>
> Matthew
>
>
>
>
>
>
>
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Date: Thursday, March 9, 2023 at 2:11 PM
> To: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>, AMBER Mailing List <amber.ambermd.org>
> Subject: {SPAM?} Re: [AMBER] CPPTRAJ, mindset xyz components
>
> *Message sent from a system outside of UConn.*
>
>
> Hi,
>
> I think 'vector minimage' should do what you want. See the manual for
> full details.
>
> -Dan
>
> On Thu, Mar 9, 2023 at 1:21 PM Matthew Guberman-Pfeffer via AMBER
> <amber.ambermd.org> wrote:
> >
> > Dear AMBER Community,
> >
> > Is there a way to print out with CPPTRAJ the x, y, and z components of the minimum displacement between two groups?
> >
> > I know that the mindist option to nativecontacts will give the minimum distance, but I need the x, y, and z components used to compute that distance. If I need to add a print statement to the source code, can you please direct me to where I should do that?
> >
> > Best,
> > Matthew
> >
> >
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Received on Fri Mar 10 2023 - 06:30:02 PST
