[gmx-users] different energies with different GROMACS versions

[Thorsten Koeddermann]

Dear all,

I performed simple simulations of TIP4P-Ew water for 500 ps with three 
different GROMACS versions, namly 3.2.1, 3.3.1 and 4.0.2. There are 1000 
molecules in the box and the temperature was 303 K at 1 bar. When I 
compare the total energies of the three equilibrated simulations I get:

-38642.4 for GROMACS 4.0.2
-38638.2 for GROMACS 3.3.1
-38491.5 for GROMACS 3.2.1

So the 3.2.1 energies deviate by ca 150 kJ/mol from the other two. If I 
completly switsh off the coulomb interactions all energies are the same.
Does anyone know a reason for that? I don't find anything about the 
3.2.1 version at the web site.

regards


 My top file and mdp files look like:

 [ defaults ]
 ; nbfunc   comb-rule   gen-pairs  fudgeLJ  fudgeQQ
     1       2          yes      0.5     0.8333

 [ atomtypes ]
 ;name   mass   charge   ptype   c6   c12
  ow            15.99940     0.00000  A     0.31643     0.68096
  hw             1.00790     0.52422  A     0.00000     0.00000
  vw             0.00000    -1.04844  A     0.00000     0.00000

 [ nonbond_params ]
 ; i    j    func        c6           c12
  ow         hw           1    0.000000E+00    0.000000E+00
  ow         vw           1    0.000000E+00    0.000000E+00
  hw         vw           1    0.000000E+00    0.000000E+00

 [ moleculetype ]
 ; molname       nrexcl
 SOL             1

 [ atoms ]
 ; nr  type resnr residue  atom  cgnr charge mass
    1   ow    1    SOL   ow    1    0.0      15.99940
    2   hw    1    SOL   hw    1    0.52422   1.00800
    3   hw    1    SOL   hw    1    0.52422   1.00800
    4   vw    1    SOL   vw    1   -1.04844   0.0

 [ settles ]
       ; ow    funct   doh     dhh
         1       1       0.09572     0.15139

 [ dummies3 ]
 ; Dummy from     funct   a                b
 4   1   2   3      1    0.1066767208   0.1066767208

 [ exclusions ]
 1       2       3       4
 2       1       3       4
 3       1       2       4
 4       1       2       3

 [ system ]
 ; Name
 Converted from moscito

 [ molecules ]
 ; Compound        #mols
SOL           1000


and

title               =  Yo                     
cpp                 =  /lib/cpp            
dt                  =  0.002                 
nsteps              =  250000           
nstcomm             =  1                  
nstxout             =  0                     
nstvout             =  0                     
nstxtcout           =  100                
nstlog              =  10000              
nstenergy           =  100               
nstlist             =  6                       
ns_type             =  grid               
coulombtype         =  pme           
fourierspacing      =  0.12           
pmeorder            =  4                  
optimize_fft        =  yes               
ewald_rtol          =  1.0e-5          
DispCorr            =  EnerPres     
constraint_algorithm=  lincs       
lincs_order         =  4
lincs_iter          =  3
lincs-warnangle     = 30
rlist               =  0.9                     
rvdw                =  0.9                  
rcoulomb            =  0.9               
Tcoupl              =  nose-hoover  
tc-grps             =  sol                   
ref_t               =  $T                     
tau_t               =  0.5                    
Pcoupl              =  parrinello-rahman  
Pcoupltype          =  isotropic              
tau_p               =  2.0                     
compressibility     =  33.0e-6         
ref_p               =  1.0                     
gen_vel             =  no                    
;gen_temp            =  303               
;gen_seed            =  1993