[gmx-users] How to use comm_mode and accelerate together?

Wang Xiaofeng canderywxf at gmail.com
Tue Sep 13 02:11:59 CEST 2011

Dear all,

To make molecules move, accelerate should be used. nstcomm is the frequency for center of mass motion removal 

But if they are used together, the molecule will not move.

I made a model system: a box of pure water. Adding accelerate to SOL in Z direction.

Firstly, comm_mode was set to no. But there was a warning during grompp:"You are not using center of mass motion removal (mdp option comm-mode),

numerical rounding errors can lead to build up of kinetic energy of the center of mass。 Net Acceleration in Z direction, will not be corrected"

The results really drift.

Then nstcomm=10 was set, the averaged velocity of water molecule in Z direction was close to zero.

I checked the tpr file using gmxdump, and found out that acc is set to 0, but accelerate   = 0.0  0.0  -0.001 is in mdout.mdp,

So How to use these two parameters together? Not only make the steady water flow but also not drift? 

Thanks a lot


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