[gmx-users] energyminimisation

gold gunaseelan gold_smith at rediffmail.com
Sat Apr 3 15:36:01 CEST 2004


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dea all,
I am using gromacs-3.2.1 for simulating a protein.I used the em.mdp file given there.when i tried to energy minimize the protien it gives the following error

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 2000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 53 steps,
but did not reach the requested Fmax < 2000.
Potential Energy  = -3.1566375e+05
Maximum force     =  2.8458027e+03 on atom 1650
Norm of force     =  1.7127547e+05
 

This is the input file i gave, 
**********************************************************************************

        User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  steep
nsteps              =  1000
;
;       Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
********************************************* 
Is this wrong,has the protein not energy minimized sufficiently.please tell what should be done? 
cheers
smith 




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