[gmx-users] Minimization problem, again!

[liu xin]

Dear GROMACS users,

My minizization problem still got no resolvment, even I restarted from make
hole, using different values for "hfm", I got almost the same message when I
try to minimize my lipid/protein system.  so I send this mail again asking
for help.

I checked the output energy, after SD minimization with my lipid/protein
system, found the values are abnormal:

##########################################################################
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 2000.
Potential Energy  =            nan
Maximum force     =            inf on atom 9614
Norm of force     =            nan
##########################################################################

Then I checked the em.log line by line, found there are two message:

##########################################################################
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)
##########################################################################

Infact I did set "constraints = none" in mdp file, and I got the same result
when changing the stepsize from 0.002 to 0.02. I searched this forum,
somebody said it is because of bad start structure, so I restarted from
makeing hole, using hfm = 5, 10, 10 then 100, 100, 150, but I still got
almost the same result, except that the atom number of "Maximum force"
varies, I am new to gromacs, I've been stuck into this problem for a week,
could anybody give me some suggestions? Any suggestions will be highly
appriciated!

Thanks in advance!
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