# Center of mass motion issue **URL:** \ **Category:** User discussions\ **Created:** [May 25, 2024, 7:15am UTC](https://gromacs.bioexcel.eu/t/center-of-mass-motion-issue/9219 "2024-05-25T07:15:17Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![Rana-1](https://avatars.discourse-cdn.com/v4/letter/r/439d5e/32.png) [@Rana-1](https://gromacs.bioexcel.eu/u/Rana-1)\ **Post date:** [May 25, 2024, 7:15am UTC](https://gromacs.bioexcel.eu/t/center-of-mass-motion-issue/9219/1 "2024-05-25T07:15:17Z")
GROMACS version: 2020.4 GROMACS modification: Yes/No Here post your question Dear users I ran a 10 ns MD for a DNA molecule. the .mdp file I used is attached. After the MD is complete, I used the commands below to prepare my .xtc and .gro files I need for trajectory analysis. gmx trjconv -s “A1\_A2\_pr.tpr” -f “A1\_A2\_pr.xtc” -o “A1\_A2\_pr\_PBC.xtc” -pbc mol -center gmx trjconv -s “A1\_A2\_pr.tpr” -f “A1\_A2\_pr.xtc” -o “A1\_A2\_pr\_PBC.gro” -pbc mol -center -dump 1 I noticed that the molecule moves. It translates and rotates. My understanding that rotation is expected but translation is not because the mdout.mdp says that center of mass motion is removed every 100 steps. **md\_pr.mdp** title = Simulations on Visual Dynamics ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 \* 5000000 = 10000 ps (10 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 10.0 ps nstvout = 0 ; save velocities every 10.0 ps nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System ; replaces xtc-grps ; Bond parameters continuation = yes ; Restarting after NPT constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rlist = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw\_switch = 1.0 rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) DispCorr = no ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = DNA Water\_and\_ions ; two coupling groups - more accurate tau\_t = 0.1 0.1 ; time constant, in ps ref\_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 2.0 ; time constant, in ps ref\_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen\_vel = no ; Velocity generation is off **mdout.mdp** ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 100 ; group(s) for center of mass motion removal comm-grps = ![Screenshot 2024-05-25 at 08.12.21](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/5cbfca8ad95005e40da45811edd37d0f201ec9fe.png) ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [May 25, 2024, 12:32pm UTC](https://gromacs.bioexcel.eu/t/center-of-mass-motion-issue/9219/2 "2024-05-25T12:32:55Z")
Dear @Rana-1 , The two things are different. The COM motion removal should be a calculation of the velocity of the COM of the whole box, and then that velocity is subtracted to all the atoms in the box, that is, you are setting to zero the velocity of the COM of the box. If I remember correctly, this makes sure that the box doesn’t accumulate kinetic energy over time due to numerical integration errors etc, which back in the day in the first MD works gave origin to the so called [flying ice cube effect](https://en.wikipedia.org/wiki/Flying_ice_cube), where the rescaling of velocities to thermostat the systems led to frozen atomic configurations and box huge linear momenta (a flying ice cube!). The removal of the COM is, very roughly, something to prevent an artifact. However, the ability of the system to diffuse around the box is something else, which is related to the nature of what you simulate. Here you have DNA in water at 300 K and I would say there is no reason to expect it to not diffuse around.