[gmx-users] (no subject)

gold gunaseelan gold_smith at rediffmail.com
Mon Apr 5 13:11:01 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"
> #else
> #include "spc.itp"
> #endif
> 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
#include "spc.itp"

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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