[gmx-users] refcoord-scaling=com

kai.exner at alumni.uni-ulm.de kai.exner at alumni.uni-ulm.de
Sun Aug 12 10:16:30 CEST 2018

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,

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