[gmx-users] COM translation

Janne Hirvi janne.hirvi at joensuu.fi
Mon Dec 5 12:48:41 CET 2005


I am trying to produce structured (stripes etc.) polymer surfaces by pressing
bulk polymer step by step between two grid surfaces. One grid surface is planar
and the other one is negative from the wanted surface structure.

I have problem with large COM translation in the direction of stripes, but
however I think that I can't use linear -option for center of mass motion
removal because the shape of the systems should/will change during simulation
from enterily planar to some modified shape.  

So do I get misinterpret simulation temperatures without COM motion removal and
what could I possibly do to solve this problem? At least there is still
vibrational and torsional motions too, but can I somehow see what is the real
temperature without COM translation? I think that g_energy ang g_traj give
temperature based on "total velocities"? 

Thanks for any help or comments! 


Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi

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