Re: distance calculation between atoms of two segments

From: Ajasja Ljubetič (
Date: Sat Jan 22 2011 - 13:48:54 CST

Dear Mingjun,

Look at the pbctools
<>specifically the pbc
unwrap command.


On Sat, Jan 22, 2011 at 17:51, mjyang <> wrote:

> Dear all,
> I performed a MD simulation for a protein+ligand+water system with
> periodic boundary conditions by NAMD. But when I calculated the distance
> between two atoms, one in ligand and the other in protein, some values of
> the distance is as large as 60 angstrom. After checking the dcd files, I
> noticed that in some frames, the ligand and protein were in different unit,
> e.g. protein in the primary unit and ligand in the neighboring image unit.
> Is anyone who encounters the same problem? Could someone please tell me how
> to fix it by distance calculation?
> Many thanks.
> Mingjun

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