[gmx-users] Does gmx distance correct for broken molecules from pbc?

[Mark Abraham]

Hi,

gmx help distance shows that there are two PBC-related options. Perhaps
your answer lies there.

Mark

On Fri, Aug 4, 2017 at 9:47 AM Ramon Crehuet <ramon.crehuet at iqac.csic.es>
wrote:

> Dear all,
>
> I have a system composed of a trimeric protein and a double stranded DNA.
> I would like to calculate the distance between the center of mass (com) of
> the protein and the com of the DNA (I am working with the NVT equilibration
> trajectory as an example). I tried:
>
>
> gmx distance -f nvt.trr -s nvt.tpr -select 'com of group Protein plus cog
> of group DNA' -xvg none -oall -rmpbc
>
> This gave distances that seem too long. Then I created a trajectory
> removing the PBC:
>
> gmx trjconv -f em.gro -s em.tpr -o whole.pdb -pbc nojump
> gmx trjconv -f nvt.trr -o whole.xtc -s whole.pdb -pbc nojump
>
> And calculated the distances again:
>
> gmx distance -f whole.xtc -s whole.pdb -select 'com of group Protein plus
> cog of group DNA' -xvg none -oall -rmpbc
>
> This gives reasonable results, different from the previous call to gmx
> distance. In an attempt to avoid calculating the whole.xtc trajectory I
> gave a pdb file that doesn't have broken molecules:
>
> gmx distance -f nvt.trr -s whole.pdb -select 'com of group Protein plus
> cog of group DNA' -xvg none -oall -rmpbc
>
> But this still gives the wrong result. I thought the flag -rmpbc would
> make molecules whole, but apparently it doesn't in my case. Is there a way
> to calculate the distance directly from the original trajectory?
>
>
> Thanks in advance,
>
> Ramon
>
>
>
> --
>
>
> Ramon Crehuet
>
> Cientific Titular (Assistant Professor)
>
> Institute of Advanced Chemistry of Catalonia IQAC - CSIC
>
> scholar.google.es/citations?user=PIHmEiwAAAAJ
> orcid.org/0000-0002-6687-382X
> publons.com/a/1018637/
> twitter.com/rcrehuet
> ramoncrehuet.wordpress.com
>
> Tel. +34 934006116 <+34%20934%2000%2061%2016>
> Jordi Girona 18-26
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