[gmx-users] Positive Coul. recip. term

Dommert Florian dommert at icp.uni-stuttgart.de
Sat Feb 25 12:43:30 CET 2012


On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote:
> Thank you both for your replies.  I currently have another ionic
> liquid running just fine on the same gromacs build (compiled the tpr
> file yesterday), so I am reluctant to conclude that the problem is
> with the linking.  Please let me know if you disagree.  
> The force field I am using was published in 2004 and has been
> validated by another group.  I have double and triple checked my itp
> files to make sure they match the force field, but it's possible there
> are still some errors there. 

Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who
validated it, I am just curious, and what is the ionic liquid ? 

Though you are constraining the hbonds, I would be cautious with the
time step of 2fs, because it might be, that the eigenfrequency of the
anionic bonds requires a shorter time step, but this should not be the
problem of a positive Coulomb energy. Have you calculated the error in
the electrostatic force ? I would suggest to tune it to a limit of 1e-3,
perhaps this resolves the problem of the positive Coulomb term.

Perhaps some 1--4 and dihedral interactions are missing in the itp file,
so assure if all of them are provided correctly.

/Flo

> I agree that this is very strange and feel that there must be
> something fundamentally wrong in the mdp file or deeper.  I have
> included my mdp file below.
> 
> 
> title               =  PMP+TFN
> cpp                 =  /lib/cpp
> constraints         =  hbonds
> integrator          =  md
> dt                  =  0.002   ; ps !
> nsteps              =  10000000   ; total 20 ns
> nstcomm             =  10
> nstxout             =  50000
> nstvout             =  50000
> nstfout             =  0
> nstlog              =  5000
> nstenergy           =  5000
> nstxtcout           =  25000
> nstlist             =  10
> ns_type             =  grid
> pbc                 =  xyz
> coulombtype         =  PME
> vdwtype             =  Cut-off
> rlist               =  1.2
> rcoulomb            =  1.2
> rvdw                =  1.2
> fourierspacing      =  0.12
> pme_order           =  4
> ewald_rtol          =  1e-5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  v-rescale
> tc_grps             =  PMP   TFN 
> tau_t               =  0.2  0.2 
> ref_t               =  300  300
> nsttcouple          =  1
> ; Energy monitoring
> energygrps          =  PMP   TFN
> ; Isotropic pressure coupling is now on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  2.0
> ref_p               =  1.0
> compressibility     =  4.5e-5
> 
> 
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  -1
> 
> 
> 
> On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian
> <dommert at icp.uni-stuttgart.de> wrote:
>         On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote:
>         > Dear all,
>         > I am trying to equilibrate a solvent of pure ionic liquid.
>          The system
>         > keeps exploding (after 2-5 ns) and I am not sure why, though
>         I believe
>         > coulombic interactions are to blame.  This is because the
>         Coul-SR term
>         > is negative, but the Coul. recip term is very positive
>         throughout the
>         > entire run (giving the entire system a positive potential
>         energy).  I
>         > think this means that the short-range electrostatics are
>         okay, but the
>         > long range electrostatics (calculated with PME) are not.
>          Does anybody
>         > have any suggestions as to why this would happen?  I have
>         used the
>         > exact same PME input parameters for another ionic liquid
>         that works
>         > just fine.  They are listed below.
>         >
>         >
>         > rcoulomb = 1.2
>         > fourierspacing = 0.12
>         > pme_order = 4
>         > ewald_rtol = 1e-5
>         >
>         
>         
>         Depends on the force field you are using. Perhaps it ist not
>         validated
>         for the ionic liquid you want to study. It is especially
>         strange, that
>         it takes so long for your system to blow up.
>         
>         Moreoever I would try to optimize the PME settings with the
>         tools,
>         g_tune_pme and g_pme_error, which give you performance and
>         accuracy of
>         the parameters, respectively.
>         
>         So perhaps with some more information I can provide more help.
>         
>         /Flo
>         
>         >
>         > Thanks!
>         > Denzil Frost 
>         > --
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>         
>         --
>         Florian Dommert
>         Dipl. - Phys.
>         
>         Institute for Computational Physics
>         University Stuttgart
>         
>         Pfaffenwaldring 27
>         70569 Stuttgart
>         
>         EMail: dommert at icp.uni-stuttgart.de
>         Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>         
>         Tel.: +49 - (0)711 - 68563613
>         Fax.: +49 - (0)711 - 68563658
>         
>         --
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> 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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