[gmx-users] monitoring position restraint energy

[David L. Bostick]

Thank you for replying David,

I have looked into using g_energy.  I am trying to monitor the position
restraint energy on a Chloride ion for a PMF calculation.  I wish to use a
position restraint b/c i want to find the PMF along a specified path .. not
between 2 groups ( i.e. Chloride and a reference group).  Therefore, I have
defined the path and wish to hold Cl- with a position restraint at a series
of points along the path.  I have tried specifying Chloride as an
energy_monitor group for mdrun, so all energy terms pertaining to Chloride
appear in the output .edr.  However, there seems to be only generic terms
like CL_LJ, long range coulomb energy, short range coulomb, etc..  There is
nothing for position restraint energy.  

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.

I use the following lines in my topology file
#ifdef RES_CL
; Position restraint for chloride PMF calculation
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       0.00000      0.00000      100000
#endif

Thanks,
David

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

> On Thu, 15 Nov 2001, David L. Bostick wrote:
> 
> >
> >Hello everyone,
> >
> >Is there a utility to extract position restraint energy data for a
> >trajectory?  
> You mean you want to compute position restraint energy for a simulation
> you ran without posres? In that case you can rerun mdrun
> (mdrun -rerun old.trr)
> mdrun then recomputes all the energies. If you are only interested in
> posres you can use real short cut-offs (no PME etc.)
> 
> If you did run with posres, g_energy will extract it from the enrgy file
> 
> >THank you to whomever responds,
> >David
> >
> >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >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	
> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> >
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> 
> 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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