[gmx-users] Energy minimization problem

[Dmitry Kovalsky]

Hi All,

I have encountered one problem if including counterions in my simulation
While minimizing a protein with 5 counterions I get the following message

"......
Step 1028, E-Pot = -4.2400537500e+05, F-max =  2.46631e+02
Step 1029, E-Pot = -4.2410303125e+05, F-max =  8.04250e+02
Negative w:  -4.807500339610e+13
z=  -7.589670500000e+06
gpa=   5.727671611336e+06, gpb=   1.845044696754e+07
a=   0.000000000000e+00, b=   9.266461607997e-07
EpotA=  -4.241030312500e+05, EpotB=  -4.240932187500e+05
Negative number for sqrt encountered (-48075003396096.000000)
Terminating minimization
 
writing lowest energy coordinates.
Maximum force:  1.31781e+03
 
Conjugate Gradients did not converge in 5000 steps
  Function value at minimum =  -4.2410e+05"
 
but when I have done this procedure wihtout counterions everything was Ok.
Here I used GROMOS96 forcefield.
What could it be?
mdp otions are:

title               =  look
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
integrator          =  cg
constraints         = none
nstcgsteep          =  5
nsteps              =  5000
nstlist             =  10
morse               =  no
ns_type             =  grid
rlist               =  0.8
rcoulomb            =  1.4
rvdw                =  1.4

;       Energy minimizing stuff
;
emtol               =  100.0
emstep              =  0.01

and protein .top files is as follows:

; Include chain topologies
#include "look_A.itp"
#include "look_B.itp"
#include "ions.itp"

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

[ system ]
; Name
GRoups of Organic Molecules in ACtion for Science in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
SOL              7418
CL-                 5

I would be greatly appreciate receiving any suggestions conserning the problem

Cheers, Dmitry