Com motion and position restraints in an NPT ensemble

User discussions
1

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). I wonder if there is any conclusion about this concern?

I really appreciate any help!

Best,

Erica

1 Like
2

I assume you mean “position restraints” and not “potential restraints”.

The solution is simply to disable center of mass motion removal.

3

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.”

4

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

5

Ah, the checking code is incorrect. You always get this error with position restraints, independently of if you remove COMM or not.

6

ok, thanks!