[gmx-users] Re: Non-equilibraium MD: simulating a moving plate.

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Mon Mar 23 01:00:52 CET 2009

Hi, have you set comm-mode = None? If no, you can set it and try again.


Zhongqiao Hu

Dept of Chemical and Biomolecular Engineering

National University of Singpore





>I want to simulate a rigid plate (wall) moving along one direction and

>reflecting all the particles it meets.


>I have made a potential only for repulsion which acts at the distances

>less than 1 nm (and equals zero at bigger ones) and bound it to a

>particle. If the plate is immovable everything goes OK. To make it go

>I use


>acc-grps                 = WAL

>accelerate               = 0 0 1


>where the acceleration is in [nm/ps2] (from the gmx manual 4.0).


>To make a plate motion insensitive to the molecules it reflects, its

>mass was set to a very big value. But during the following run the

>plane moved very slowly while all other particles in the system have

>obtained an acceleration at the same direction. Even those ones which

>are to far to interact with a plate. Why? Then if the mass of the

>plate is reduced the above effect is not so pronounced but then the

>plate becomes very sensible to the interactions, so its motion is not

>as we want...

>If the acceleration is given in  [nm/ps2], how the mass can influence

>the motion? I thought this value is just added to the value obtained

>from the interations, but it's evidently not true here.


>Please let me know if it's possible in gromacs to make such moving

>plate I described and if so, what is a good practice to simulate this




>Thank you,






>Vitaly V. Chaban, Ph.D. (ABD)

>School of Chemistry

>V.N. Karazin Kharkiv National University

>Svoboda sq.,4, Kharkiv 61077, Ukraine

>email: chaban at univer.kharkov.ua,vvchaban at gmail.com

>skype: vvchaban, mob.: +38-097-8259698



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