[gmx-users] SD and CG EM!

[Luciano Tavares]

 Hi Martina Bertsch and gmx-users,

 Thanks for advise...

 Well, I'm sorry my persistence. I have tried to do the protocol that
Martina had adviced me. However, I have performed EM just putting only the
protein, without pbc such as below:

title               =  EM
cpp                 =  /lib/cpp
integrator          =  cg   ; initially with steep
nsteps              =  1000
nstcgsteep          =  0.01
emtol               =  27000 ; starting with 50000, 40000 and after 30000
emstep              =  0.001

pbc                 =  no
nstcomm             =  1
ns_type             =  simple
nstlist             =  0
rlist               =  0.0
rcoulomb            =  0.0
rvdw                =  0.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

But, the message have appeared again in this stage, with emtol = 27000
kJ*mol^-1*nm^-1:

Step 9, E-Pot = 1.0114848125e+06, Fmax =  5.40031e+05, atom = 1668
Step 10, E-Pot = 1.0114861250e+06, Fmax =  5.19963e+05, atom = 1863
Negative w:  -5.214692788374e+23
z=  -1.151546032128e+12
gpa=   6.963870543712e+11, gpb=   2.653018202711e+12
a=   0.000000000000e+00, b=   1.102683569454e-10
EpotA=   1.011486125000e+06, EpotB=   1.011651562500e+06
Negative number for sqrt encountered (-521469278837438404362240.000000)
Terminating minimization

I guess it wouldn't be some kind of mistake with the structure,
because I have already performed a pdb2gmx command with no problems. What
the hinted of the parameters (or terms) above?!

Well, very very thanks in advance...

Luciano

PS: I'm sorry, my last messages were with problems in the format.
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##      Luciano Tavares da Costa * ltcosta at universiabrasil.net      ##
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