[gmx-users] refcoord-scaling=com

[Mark Abraham]

Hi,

As you see in the docs
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-refcoord-scaling
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.

Mark

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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