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From: Mark Zottola (mzottola_at_gmail.com)
Date: Sun Sep 20 2020 - 20:17:39 CDT
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I was told the coordinate files given to me were generated from a psf and
dcd files extracted using the "Save Coordinates" command in VMD. I
received a copy of these files and tried to extract them myself. I do not
see where there is an option to "unwrap".
Can you be a bit more explicit with your guidance?
Thanks.
On Mon, Sep 21, 2020 at 7:22 AM Bassam Haddad <bhaddad_at_pdx.edu> wrote:
> Try unwrapping your coordinates prior to extracting them.
>
> ~ Bassam
>
> On Sun, Sep 20, 2020 at 1:37 AM Mark Zottola <mzottola_at_gmail.com> wrote:
>
>> I am tracking the path of ions in an MD simulation. I used VMD to
>> extract the coordinates from each frame and write it out to a PDB file.
>>
>> I have run into a problem where suddenly one coordinate (usually y or z)
>> suddenly flips sign. In other words in one frame the z-coordinate would be
>> -15.xxx and the next frame the z-coordinate is +16.xxx. The other
>> coordinates remain close in value and identical in sign to the previous
>> coordinates. This continues for an indeterminate number of steps then the
>> offending coordinate flips back again.
>>
>> I am surmising this has something to do with crossing over a boundary as
>> we are using periodic boundary conditions. Is there any way to obviate
>> this issue?
>>
>> Thanks for any advice.
>>
>
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