[gmx-users] Gromacs 4.5.4 and Gromacs 4.5.5 give different results

[sarupria]

Hello all, 

I have a naphthalene + water system which I want to run a NPT simulation of.
The system has been energy mininimized. When I run the NPT simulation using
gromacs 4.5.5 the simulation runs fine, but when I attempt to run the same
simulation using 4.5.4 it crashes with lincs error.  We have tried various
things like energy minimizing multiple times using 4.5.4 but it still
crashes. I have also changed the thermostat and barostat to Berendsen, the
problem persists. 

Has anything changed between the two versions that could lead to this
trouble? I am pasted the mdp file below and also the last few lines of the
error message I get from Gromacs 4.5.4. 

Thanks for your help. 
Sapna 

************ MDP FILE ********* 
title               =  NPH + water              ; a string 
dt                  =  0.002                    ; time step 
nsteps              =  12500000                  ; number of steps 
comm-grps           =  system 
comm-mode           =  Linear 
nstcomm             =  10                       ; reset c.o.m. motion 
nstxout             =  000                      ; write coords 
nstvout             =  000                      ; write velocities 
nstlog              =  2500                     ; print to logfile 
nstenergy           =  500                      ; print energies 
xtc_grps            =  System 
nstxtcout           =  1000 
nstlist             =  10                       ; update pairlist 
ns_type             =  grid                     ; pairlist method 
coulombtype         =  PME 
rvdw                =  1.00                     ; cut-off for vdw 
rcoulomb            =  1.00                     ; cut-off for coulomb 
rlist               =  1.00                     ; cut-off for coulomb 
Tcoupl              =  Nose-Hoover 
ref_t               =  280.0 
tc-grps             =  System 
tau_t               =  0.5   
DispCorr            =  EnerPres                 ; long range correction 
gen_vel             =  yes                       ; generate init. vel 
gen_temp            =  280                      ; init. temp. 
gen_seed            =  372340                   ; random seed 
constraints         =  h-bonds                   ; constraining bonds with H 
constraint_algorithm = lincs 
refcoord-scaling    =  no 
Pcoupl              =  Parrinello-Rahman 
Pcoupltype          =  isotropic                ; pressure geometry 
tau_p               =  1.0                      ; p-coupoling time 
compressibility     =  4.5e-5                   ; compressibility 
ref_p               =  1.0                      ; ref pressure 
nsttcouple          =  1 
nstpcouple          =  1 
***************** END MDP File *************** 

*********** Error Message ************* 
Program mdrun_sp, VERSION 4.5.4 
Source code file: constr.c, line: 176 

Fatal error: 
Too many LINCS warnings (4811) 
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file 
or set the environment variable GMX_MAXCONSTRWARN to -1, 
but normally it is better to fix the problem 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors
------------------------------------------------------- 


*********** End Error Message ************* 



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