# Com motion and position restraints in an NPT ensemble **URL:** \ **Category:** User discussions\ **Tags:** restraints\ **Created:** [March 18, 2021, 6:49pm UTC](https://gromacs.bioexcel.eu/t/com-motion-and-position-restraints-in-an-npt-ensemble/1778 "2021-03-18T18:49:45Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Erica](https://avatars.discourse-cdn.com/v4/letter/e/9dc877/32.png) [@Erica](https://gromacs.bioexcel.eu/u/Erica)\ **Post date:** [March 18, 2021, 6:49pm UTC](https://gromacs.bioexcel.eu/t/com-motion-and-position-restraints-in-an-npt-ensemble/1778/1 "2021-03-18T18:49:45Z")
GROMACS version: 2020 GROMACS modification: No Hi, As part of a MD-based model refinement protocol, I want to run long simulations in **NPT** ensemble applying potential restraints to C-alpha atoms. However, I see that Berk previously raised the question about possible artifacts for doing that in NPT without removing the center of mass motion ([Re: [gmx-users] com motion and position restraints may cause artifacts](https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg40058.html)). I wonder if there is any conclusion about this concern? I really appreciate any help! Best, Erica ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [March 22, 2021, 1:34pm UTC](https://gromacs.bioexcel.eu/t/com-motion-and-position-restraints-in-an-npt-ensemble/1778/2 "2021-03-22T13:34:41Z")
I assume you mean “position restraints” and not “potential restraints”. The solution is simply to disable center of mass motion removal. ---
**Author:** ![Erica](https://avatars.discourse-cdn.com/v4/letter/e/9dc877/32.png) [@Erica](https://gromacs.bioexcel.eu/u/Erica)\ **Post date:** [March 22, 2021, 2:24pm UTC](https://gromacs.bioexcel.eu/t/com-motion-and-position-restraints-in-an-npt-ensemble/1778/3 "2021-03-22T14:24:32Z")
Hi Hess, Thank you for the reply. Yes, I meant applying a position restraint potential on C-alpha. My question was based on your own concern: “I realize now that we should check if there are no other artifacts when doing equilibration with position restraints in an NPT ensemble without comm-removal. I expect NVT should be fine without comm-removal.” ---
**Author:** ![Erica](https://avatars.discourse-cdn.com/v4/letter/e/9dc877/32.png) [@Erica](https://gromacs.bioexcel.eu/u/Erica)\ **Post date:** [March 22, 2021, 2:31pm UTC](https://gromacs.bioexcel.eu/t/com-motion-and-position-restraints-in-an-npt-ensemble/1778/4 "2021-03-22T14:31:47Z")
Taking this opportunity, I would like to make one related question :) I ran a NVT simulation (Nose-Hoover) using position restraints and disabled center of mass removal (comm-mode=None). I still get this Note, though: “Removing center of mass motion in the presence of position restraints might cause artifacts. When you are using position restraints to equilibrate a macro-molecule, the artifacts are usually negligible.” Am I possibly implicitly removing center of mass motion anywhere here? define = -DPOSRES\_CA\_FB -DPOSRES\_FC\_CA=100.0 -DPOSRES\_SUB\_FB -DPOSRES\_FC\_SUB=100.0 integrator = md-vv dt = 0.004 nsteps = 8000000 nstxtcout = 10000 nstvout = 10000 nstfout = 10000 nstcalcenergy = 100 nstenergy = 1000 nstlog = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 coulombtype = pme rcoulomb = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw\_switch = 1.0 rvdw = 1.2 tcoupl = Nose-Hoover ;berendsen ;V-rescale tc\_grps = SYSTEM tau\_t = 1.6 ; 1.0; at least 20 times larger than nsttcouple\*dt (0.08) ref\_t = 360.15 constraints = h-bonds constraint\_algorithm = LINCS comm-mode = None gen-vel = no gen-temp = 360.15 gen-seed = -1 continuation = yes ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [March 22, 2021, 2:52pm UTC](https://gromacs.bioexcel.eu/t/com-motion-and-position-restraints-in-an-npt-ensemble/1778/5 "2021-03-22T14:52:46Z")
Ah, the checking code is incorrect. You always get this error with position restraints, independently of if you remove COMM or not. ---
**Author:** ![Erica](https://avatars.discourse-cdn.com/v4/letter/e/9dc877/32.png) [@Erica](https://gromacs.bioexcel.eu/u/Erica)\ **Post date:** [March 22, 2021, 2:54pm UTC](https://gromacs.bioexcel.eu/t/com-motion-and-position-restraints-in-an-npt-ensemble/1778/6 "2021-03-22T14:54:44Z")
ok, thanks!