[gmx-users] COM translation

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 5 14:29:59 CET 2005

Janne Hirvi wrote:

>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"? 
Are you interested in the final structure only? In that case you could 
try some kine of simulated annealing protocol.

>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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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