[gmx-users] refcoord-scaling=com

Mark Abraham mark.j.abraham at gmail.com
Sun Aug 12 14:33:38 CEST 2018


As you see in the docs
there are different reference coordinates chosen on your two fragments. The
2018 series of GROMACS prompts you to choose what those coordinates are
with grompp -r, which will probably permit the kind of continuity you seek.
The feature was always there, but defaulted to the coordinates of grompp
-c. Of course the simulations aren't physical, either way.


On Sun, Aug 12, 2018, 11:16 <kai.exner at alumni.uni-ulm.de> wrote:

> Dear Gromacs Users,
> I'm performing MD simulations (NPT) with position restraints for part
> of the system, thereby using the refcoord-scaling=com option in the
> mdp-file. After the MD run has finished and I'm restarting the MD by
> taking the last frame and simply extending the simulation time, I
> obtain the following problem:
> When calculating certain properties, such as RMSD, radius of gyration
> or solvent accessible surface area for the atoms with position
> restraints, I obtain an artificial jump in these quantities when
> comparing the two subsequent MD runs. This jump directly occurs at the
> beginning of the second (extended) MD run.
> I ascribe this jump to the rescaling of the com, since the center of
> masses in the first frame of the second (extended simulation) is
> different than the center of mass in the last frame of the first
> simulation. I was also translating the center of masses from the first
> frame of the second simulation to the last frame of the first
> simulation and then recalculating the above-mentioned properties,
> however, without success.
> Do you know how to solve this problem? Actually, I verified that this
> jump is an artefact, since I was running one of the MDs for the double
> time and then the jump does not occur. This jump only arises, when I
> extend the time of a MD simulation.
> I would be thankful for any help and reply,
> Kai
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