[gmx-users] Re: COM translation

[Janne Hirvi]

Hello David!

I don't understand how could I use simulated annealing protocol. Yes, I am
interested only in the final structure, but still I have no clue what do you
mean. My problem is that I get COM translation about 20-25nm/ns without COM
motion removal and I was interested how much this effects on my simulation
temperature. If I am right, the influence is not so "significant". At least the
system is not frozen and still have vibrations and other high frequency motions
as it really should have at high temperature (450-600K). 

Janne

> 
> Janne Hirvi wrote:
> 
> >Hello!
> >
> >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
> >
>
>------------------------------------------------------------------------------
> >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
>
>------------------------------------------------------------------------------
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the 
> >www interface or send it to gmx-users-request at gromacs.org.
> >  
> >
> 
> 
> -- 
> David.
> ________________________________________________________________________
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++