Bug #1339
Center of mass drift with Nose-Hoover, MTTK and md-vv
Description
Simulation of single long polymer chain shows huge center of mass drift during microsecond simulation.
The very same system has been simulated with md integrator and nose-hoover and parrinello-rahman with identical settings and no significant drift has been detected.
Here I have attached the simulation files and the architecture used for running simulation. The plot of the center of mass velocity is larger than 10 mb, so I could not attach it.
I have seen your discussion in bug#165, so thought yo might be interested in this one too.
Related issues
History
#1 Updated by ABolfazl Noorjahan over 7 years ago
I am attaching the topol.top file in case if you need it.
#2 Updated by David van der Spoel over 7 years ago
Is it center of mass of the whole system? That is, is the box changing shape?
#3 Updated by Szilárd Páll over 7 years ago
Have you tried 4.6.3?
#4 Updated by ABolfazl Noorjahan over 7 years ago
Yes, the center of mass of the whole system (which is a polymer chain with 400 monomer) is drifting. The box shape stays cubic and with a bit oscillation due to pressure control (The density is constant with correct value for polymer chain at all specified temperatures.).
I did simulations with 4.6 on a cluster and the only version available was 4.6 and below. If you think that may cause problem I can request an upgrade and repeat the calculations.
#5 Updated by Michael Shirts over 7 years ago
What's the shortest time scale over which it is statistically significant?
ABolfazl Noorjahan wrote:
Yes, the center of mass of the whole system (which is a polymer chain with 400 monomer) is drifting. The box shape stays cubic and with a bit oscillation due to pressure control (The density is constant with correct value for polymer chain at all specified temperatures.).
I did simulations with 4.6 on a cluster and the only version available was 4.6 and below. If you think that may cause problem I can request an upgrade and repeat the calculations.
#6 Updated by ABolfazl Noorjahan over 7 years ago
Here I am attaching the Velocity of center of mass during time. I tried to zoom in to see the time scale on which the diversion starts.
#7 Updated by David van der Spoel over 7 years ago
Is your molecule cyclic?
#8 Updated by Michael Shirts over 7 years ago
David van der Spoel wrote:
Is your molecule cyclic?
It's a single polyethylene chain. I'm not sure what to make of that, other than perhaps something odd might happen with temperature groups. Note that it's using h-bonds, not all bonds.
Currently, it looks like an abrupt 1 nm vdw cutoff, which could give artifacts.
I'd like to see it run with (and I am trying a short version of this now).
nstcalctcoupl = 1
nstcalpcoupl = 1
nstcalcenergy = 1
nstcomm = 1
To remove any weird issues with properties being calculated only every N steps.
#9 Updated by Michael Shirts over 7 years ago
I started running this but realized that it may take a rather long time to check this -- it's running on my laptop at 2 ns/day, and it's not clear the issues would really be distinguishable for 1-2 days. Error cases that can be distinguished are usually better. . .
So far (20-30 ps in), it appears that the COM velocities are about 10x times larger for md-vv, using nstcomm = 100. For md/pr, it's down at 5^10-6, while for md-vv, it's more like 5^10-5, occasionally 1^10-4. This seems somewhat suspicious. I'll keep investigating.
#10 Updated by Michael Shirts over 7 years ago
Interestingly, it seems to be happening when nstcomm = 1 as well, and also when MTTK is off. If it's just that it's outputting the velocities at a different place in the loop, then that's not a big deal. I'll let it go overnight and see if the drift continues, and investigate the code further.
#11 Updated by Erik Lindahl almost 7 years ago
- Assignee changed from David van der Spoel to Michael Shirts
- Target version changed from 4.6.x to 5.x
#12 Updated by Erik Lindahl over 5 years ago
- Target version changed from 5.x to future
Any update on the investigation? ;-)
#13 Updated by Mark Abraham almost 3 years ago
- Related to Feature #1137: Proposal for integrator framework (do_md) in future GROMACS added