[gmx-users] RMSD of energy minimized structure

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Sep 30 08:41:47 CEST 2016

Hi Surya,

The first part ss a warning, not an error. It also says (implicitly) that
if the molecules are not broken across PBC then there's nothing to worry
about whatsoever. So just assert that your molecules are not split over
PBC. Have a look at the trajectory. If there are frames with one part of
the structure on one side of the box and another on the other side, then
run gmx trjconv -pbc mol on the trajectory, using a .tpr file as reference

Why it doesn't give any output is impossible to say without getting more
information. Please paste the command line and the output from the terminal
in a mail and send that to us, so we can see what happened.



On Fri, Sep 30, 2016 at 7:33 AM, Seera Suryanarayana <palusoori at gmail.com>

> Dear gromacs users,
> I have done energy minimization of clustered PDBs. When I try to
> calculate the RMSD between the minimized clustered PDB and the
> starting structure of MD simulations I got the following warning.
> If there are molecules in the input tarjectory file that are broken
> across periodic boundaries, they cannot be made whole (or treadted as
> whole) without you providing a run input file.
> I did not get what does it mean. I have not get any output for RMSD.
> Where I did wrong? Kindly tell me.
> Thanks in advance
> Surya
> Graduate student
> India.
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Tsjerk A. Wassenaar, Ph.D.

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