<P>
dear sir ,<BR>
Iam using gromacs 3.2.1<BR>
I changed the following in em.mdp file as<BR>
<BR>
define = -DFLEXIBLE and ran energy minimisation but it converged as <BR>
<BR>
Stepsize too small, or no change in energy.<BR>
Converged to machine precision,<BR>
but not to the requested precision Fmax < 2000<BR>
<BR>
Double precision normally gives you higher accuracy.<BR>
<BR>
writing lowest energy coordinates.<BR>
<BR>
Steepest Descents converged to machine precision in 202 steps,<BR>
but did not reach the requested Fmax < 2000.<BR>
Potential Energy = -4.0429609e+05<BR>
Maximum force = 4.6900386e+03 on atom 1650<BR>
Norm of force = 1.4885711e+04<BR>
<BR>
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 <BR>
<BR>
> ; Include water topology<BR>
> #ifdef FLEX_SPC<BR>
> #include "flexspc.itp"<BR>
> #else<BR>
> #include "spc.itp"<BR>
> #endif<BR>
> <BR>
> then you can try with this file:<BR>
> <BR>
> <BR>
> title = xxxx<BR>
> cpp = /lib/cpp<BR>
> include = -I../top<BR>
> define = -DFLEX_SPC<BR>
<BR>
I would like to point out that tis has been changed a bit in 3.2<BR>
If you use spc water this still will work, but for other models the more<BR>
generic way of writing is:<BR>
<BR>
#include "water.itp" (either tip3p, tip4p, spc, spce)<BR>
<BR>
define = -DFLEXIBLE<BR>
<BR>
But i didnot find this in top file<BR>
<BR>
; Include water topology<BR>
#include "spc.itp"<BR>
<BR>
#ifdef POSRES_WATER<BR>
I found these terms missing as specified by u above.<BR>
sir please suggest whats wrong .is protein minimized properly.thanks in advance -gsmith
</P>
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