Re: Extra frame at start of each trajectory

From: Josh Vermaas (
Date: Wed Aug 05 2020 - 14:33:43 CDT

Hi Ethan,

How did you load this? In VMD, an extra frame that doesn't have pbc
information usually comes from loading the pdb file, which will load in the
coordinates. If you load in the dcd file afterwards, the files from the dcd
will be appended. NAMD *always* writes box information in its dcds, so I
don't think this is NAMD's doing.


On Wed, Aug 5, 2020 at 1:25 PM Ethan Croitoru <> wrote:

> Hello,
> I am running a Martini coarse-grained system with NAMD, built following
> the tutorial (
> My
> system is a protein in a membrane, so I used the conf files for the extra
> example M2-channel to run minimization and equilibration. The tutorial
> splits equilibration into 5 jobs, and for the first 2 jobs everything is
> normal, but at the third job there is an extra frame at the beginning of
> the trajectory that does not have periodic images (as I have set pbc). The
> only difference in the 2nd and 3rd job's conf file is the
> constraint scaling and input and output names, so I don't understand how
> this issue started to occur, but every job after the 3rd equilibration job
> has included that extra frame. The 2nd and 3rd equilibration job both run
> for the same time, but the 3rd trajectory has the extra frame in addition
> to the simulation with regular pbc, as in the 3rd trajectory has an added
> frame, rather than a frame with bad pbc. Can anyone explain why this is
> happening or how to stop it?
> Best,
> Ethan

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