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