[gmx-users] monitoring position restraint energy

David L. Bostick dbostick at physics.unc.edu
Thu Nov 15 23:38:34 CET 2001

Hi David,

Thanks for the help.  I think that's the best bet.  So far I have been
using g_traj for the coordinates.  I just think it would be nice to have
direct access to the energy.  I used the pull code to generate starting
structures, but in the end, I have a very complex reaction coordinate for
Chloride.  The pull code only helps to calculate the PMF along a reaction
coordinate between two groups.  When there is some arbitrary reaction
coordinate it seems that generating starting structures is best.  It will
also allow me to sample the coordinate points for a longer period of time
for better statistics...  

Once again.. thanks,

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Thu, 15 Nov 2001, David van der Spoel wrote:

> On Thu, 15 Nov 2001, David L. Bostick wrote:
> >I have thought about simply printing out the coordinates of Chloride and
> >calculating the restraint energy myself, but it would be nice if I could
> >just get this directly.  The manual says g_energy will give distance
> >restraint data, but nothing about position restraint data.
> You can do that with g_traj, and then a simple perl script or so will
> compute the distance for you. Isn't there some PMF functionality in the
> pulling stuff? Check the manual as I've never used it...
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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