[gmx-users] SDS micelle

[Aina Quintilla]

Dear gromacs users,

I am trying to simulate a micelle of SDS in water.
my simulation is crashing after some picoseconds ... there are LINCS warnings 
and then the system is blowing apart

the topology for 1 ds molecule i made:

#include "ffG43a1.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    
chargeB      massB
     1          S      1    SDS     S1      1      1.284      32.06   ; qtot 
1.284
     2          O      1    SDS     O1      1     -0.654    15.9994   ; qtot 
0.63
     3          O      1    SDS    O12      1     -0.654    15.9994   ; qtot 
-0.024
     4         OM      1    SDS     OH      1     -0.459    15.9994   ; qtot 
-0.483
     5         OM      1    SDS    O13      1     -0.654    15.9994   ; qtot 
-1.137
     6        CH2      1    SDS     C1      1      0.137     14.027   ; qtot 
-1
     7        CH2      1    SDS     C2      1          0     14.027   ; qtot 
-1
     8        CH2      1    SDS     C3      1          0     14.027   ; qtot 
-1
     9        CH2      1    SDS     C4      1          0     14.027   ; qtot 
-1
    10        CH2      1    SDS     C5      1          0     14.027   ; qtot 
-1
    11        CH2      1    SDS     C6      1          0     14.027   ; qtot 
-1
    12        CH2      1    SDS     C7      1          0     14.027   ; qtot 
-1
    13        CH2      1    SDS     C8      1          0     14.027   ; qtot 
-1
    14        CH2      1    SDS     C9      1          0     14.027   ; qtot 
-1
    15        CH2      1    SDS    C10      1          0     14.027   ; qtot 
-1
    16        CH2      1    SDS    C11      1          0     14.027   ; qtot 
-1
    17        CH3      1    SDS    C12      1          0     15.035   ; qtot 
-1

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     2    gb_24
    1     3     2    gb_24
    1     4     2    gb_24
    1     5     2    gb_24
    4     6     2    gb_18
    6     7     2    gb_26
    7     8     2    gb_26
    8     9     2    gb_26
    9    10     2    gb_26
   10    11     2    gb_26
   11    12     2    gb_26
   12    13     2    gb_26
   13    14     2    gb_26
   14    15     2    gb_26
   15    16     2    gb_26
   16    17     2    gb_26

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     7     1 
    2     6     1 
    3     6     1 
    4     8     1 
    5     6     1 
    6     9     1 
    7    10     1 
    8    11     1 
    9    12     1 
   10    13     1 
   11    14     1 
   12    15     1 
   13    16     1 
   14    17     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            
c3
    2     1     3     2    ga_28
    2     1     4     2    ga_28
    2     1     5     2    ga_28
    3     1     4     2    ga_28
    3     1     5     2    ga_28
    4     1     5     2    ga_28
    1     4     6     2    ga_25
    4     6     7     2    ga_29
    6     7     8     2    ga_12
    7     8     9     2    ga_12
    8     9    10     2    ga_12
    9    10    11     2    ga_12
   10    11    12     2    ga_12
   11    12    13     2    ga_12
   12    13    14     2    ga_12
   13    14    15     2    ga_12
   14    15    16     2    ga_12
   15    16    17     2    ga_12

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            
c3            c4            c5
    2     1     4     6     1    gd_11
    1     4     6     7     1    gd_12
    4     6     7     8     1    gd_17
    6     7     8     9     1    gd_17
    7     8     9    10     1    gd_17
    8     9    10    11     1    gd_17
    9    10    11    12     1    gd_17
   10    11    12    13     1    gd_17
   11    12    13    14     1    gd_17
   12    13    14    15     1    gd_17
   13    14    15    16     1    gd_17
   14    15    16    17     1    gd_17

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"

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

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
DS 

[ molecules ]
; Compound        #mols
Protein             1


and the parameters that i use to run a simulation, after a long energy 
minimization:


constraints         =  all-bonds
integrator          =  md
dt                  =  0.0005	; ps !
nsteps              =  20000	
nstcomm             =  1
nstxout             =  10
nstvout             =  1000
nstfout             =  10
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  1.4
rvdw                =  1.4
fourierspacing      =  0.12
pme_order           =  4
ewald_rtol          =  1e-5
Tcoupl             =  berendsen
tau_t              =  0.1   
tc-grps            =  system
ref_t              =  100  
gen_vel             =  yes
gen_temp            =  100
gen_seed            =  173529


could you please tell me if there is something wrong? i would be very very 
thankfull to any suggestion!