[gmx-users] box explodes when using PME

[Attila Borics]

Hi,

My simulation crashed several times. As I checked everything it 
turned out it has 2 possible causes.
One is this message from flog: 

**************************************************************************

           Step           Time         Lambda      Annealing
         138000      276.00000        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.009921     29     30   0.002540
        After LINCS         0.000026     20     22   0.000011

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14    
Coulomb-14
    5.65977e+01    4.01335e+01    1.56962e+01    1.10161e+01   
7.09566e+00
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic
En.
   -1.74165e+02   -4.26500e+00   -6.57856e+03   -6.62645e+03   
1.12548e+04
   Total Energy    Temperature Pressure (bar)
    4.62831e+03    2.99177e+02    4.60669e+01

Grid: 28 x 28 x 28 cells
WARNING: your box is exploding! (ncells = 21952)

*************************************************************************

Now I run this job on only 1 processor instead of a 4 membered ring and
it seems to be OK (I mean it keeps running), but there`s definitely 
something wrong with this: I keep getting this previous error message
in flog.

Here`s my .mdp, Is there anything I`m doing wrong?

;	User aborics
;	Thu 1/31/02
;	Input file
;
title               =  DDKG
warnings            =  10
cpp                 =  /lib/cpp
constraints         =  all-bonds
constraint_algorithm     = Lincs
integrator          =  md
tinit               =  0.0
dt                  =  0.002	; ps !
nsteps              =  12550000	; total 25.1 ns
nstcomm             =  1
; output
nstxout		    =  1000
nstxtcout           =  0
nstvout             =  2000
nstfout             =  5000
nstlog		    =  1000
nstenergy           =  1000
;
nstlist             =  10
ns_type             =  grid
deltagrid           =  2
; eeltype	  
rlist               = 0.9
coulombtype         = PME
epsilon_r	    = 78
rcoulomb            = 0.9
vdwtype	            = cut-off
rvdw                = 0.9
fourierspacing      = 0.12
pme_order           = 4
ewald_rtol          = 1e-5
; box type
pbc                   = xyz
; Temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps		    =  Protein	SOL  NA+  CL-
tau_t               =  0.1	0.1  0.1  0.1
ref_t               =  300	300  300  300
; Energy monitoring
energygrps          =  Protein  SOL
; Pressure coupling
Pcoupl              =  Berendsen
pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


Please, help.

Thanks

Attila