[gmx-users] COM-COM distance: PBC problem

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 17 08:57:01 CEST 2016

Hi Arnost,

When you fit with rotation the coordinates and the box are not on par
anymore. Anything you do after that tries using PBC will fail. I guess that
Plumed is trying to use the box to get the COM-COM distance. The only
(practical) solution: don't fit.



On Aug 17, 2016 00:24, "Arnost Mladek" <arnost.mladek at gmail.com> wrote:

> Dear Plumed users,
> I've encountered one problem I'm unable to resolve. I use combination of
> Gromacs 5.0.4 and Plumed 2.1.3 and what I want is to calculate restrained
> distance between two center of masses (COMs) corresponding to two chains
> within a dimeric protein. If I let Plumed to calculate COM-COM distances
> "on-the-fly" (ie. during the simulation), I get correct results, let say
> distances in the interval of (4,9 ; 5.3) with the average value of 5.1 nm
> corresponding to the minimum of the restraining potential.
> If I use Plumed as a stand-alone software and calculate the distances
> along the trajectory via "plumed driver --mf_xtc trajectory.xtc --plumed
> pl.dat", I get the same correct results. Up to this point, no problem.
> However if I fit (rot+trans) the trajectory frames to chain-A using
> GROMACS trjconv command (trjconv -f trajectory.xtc -s reference.tpr -o
> fitted_trajectory.xtc -fit rot+trans -center) and then run the plumed
> driver to calculate the distances from the fitted trajectory there are huge
> jumps of several nm. It is obvious that the problem is somehow associated
> with PBC and "WHOLEMOLECULES STRIDE=1 ENTITY0=protein" command within the
> plumed script is unable to resolve it. I've tried various trajectory
> transformations as suggested on GROMACS web page (http://www.gromacs.org/
> Documentation/Terminology/Periodic_Boundary_Conditions), like "-pbc mol
> -ur compact", "-pbc whole", "-pbc nojumps", etc. but nothing helped. As I
> am unable to get the COM-COM distances using GROMACS alone, I am not sure
> whether the problem relates to GROMACS or Plumed.
> Thank you so much for your help.
> AM
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list