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

[Justin Lemkul]

On 6/27/13 2:30 PM, sarupria wrote:
> 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.
>

Well, according to the release notes 
(http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x), in version 
4.5.5:

"Many small fixes which avoid termination with fatal errors or crashes in mdrun 
and tools."

Small bugs are constantly getting fixed.  I see no compelling reason to use an 
outdated version (4.5.4) when a slightly less outdated version (4.5.5) works 
correctly.

-Justin

> 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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>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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