gold_smith at rediffmail.com
Mon Apr 5 13:11:03 CEST 2004
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dear sir ,
Iam using gromacs 3.2.1
I changed the following in em.mdp file as
define = -DFLEXIBLE and ran energy minimisation but it converged as
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.
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 202 steps,
but did not reach the requested Fmax < 2000.
Potential Energy = -4.0429609e+05
Maximum force = 4.6900386e+03 on atom 1650
Norm of force = 1.4885711e+04
Previously i had given define =-DFLEX_SPC it gave the same error but it converged in 57 steps.I looked in one of ur old reply,in which u have asked to see toplogy file
> ; Include water topology
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #include "spc.itp"
> then you can try with this file:
> title = xxxx
> cpp = /lib/cpp
> include = -I../top
> define = -DFLEX_SPC
I would like to point out that tis has been changed a bit in 3.2
If you use spc water this still will work, but for other models the more
generic way of writing is:
#include "water.itp" (either tip3p, tip4p, spc, spce)
define = -DFLEXIBLE
But i didnot find this in top file
; Include water topology
I found these terms missing as specified by u above.
sir please suggest whats wrong .is protein minimized properly.thanks in advance -gsmith
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