[gmx-developers] Still one question about pme-user with user potential table and energygroup

Mark Abraham mark.j.abraham at gmail.com
Thu May 31 17:57:54 CEST 2018


This would be a thread better suited to gmx-users, since it does not relate
to developing GROMACS.

You will be able to understand better if you use mdrun -rerun to compute
the energy for single frames with e.g. single particles at distances you
determine in advance. Examining averages from simulations makes it hard to
observe that you are computing what you expect. :-)

The SR component is not the same as the contribution from your table,
because the long-range component of PME also computes small contributions
at short distances. Thus Berk's comment that in the group scheme the PME
mesh contribution (ie at short range) is subtracted by mdrun from your
table to form the tables it actually uses. Thus the total interaction at
short range is what you specified in the original table, and 1/r at greater


On Tue, May 29, 2018 at 5:12 PM Du, Yu <duyu at sioc.ac.cn> wrote:

> Dear Prof. Hess,
> If I use normal table6-12.xvg for the system and zero for coul in user
> Protein-LIG table, should Coul-SR of Protein-LIG in log file be zero or
> something else?
> I'm now a bit confused of previous post of your explaination
> <https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-October/116418.html>
> "*All you need to know is that up to the cut-off **distance, you exactly
> get the interaction you set in the table. Beyond **the cut-off you get
> 1/r.*"
> and the manual
> <http://manual.gromacs.org/documentation/2016-current/user-guide/mdp-options.html#mdp-value-coulombtype=PME-User>
> "The PME mesh contribution is subtracted from the user table by gmx mdrun
> <http://manual.gromacs.org/documentation/2016-current/onlinehelp/gmx-mdrun.html#gmx-mdrun>
> "
> The following shows the log file using normal table6-12.xvg for system and
> zero coul (1/r = 1/r^2 = 0) table for Protein-LIG, which indicates that
> Coul-SR of Protein-LIG is not zero. Is this correct?
>         <======  ###############  ==>
>         <====  A V E R A G E S  ====>
>         <==  ###############  ======>
>         Statistics over 5001 steps using 51 frames
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
>     1.40558e+03    3.54366e+03    4.51051e+03    2.20736e+02    1.56122e+03
>      Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
>     1.97118e+04    5.38376e+04   -4.25523e+05   -6.57729e+04   -4.06504e+05
>     Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
>     7.55000e+04   -3.31004e+05   -3.30639e+05    3.00015e+02   -3.96800e+00
>    Constr. rmsd
>     0.00000e+00
>    Total Virial (kJ/mol)
>     2.54108e+04    9.83166e+01    3.71371e+01
>     1.00317e+02    2.49036e+04   -1.06969e+02
>     3.08843e+01   -1.09834e+02    2.52938e+04
>    Pressure (bar)
>    -2.99929e+01   -1.19294e+01   -1.09946e+01
>    -1.21497e+01    2.62908e+01    1.50508e+01
>    -1.03063e+01    1.53662e+01   -8.20183e+00
>   Epot (kJ/mol)        Coul-SR          LJ-SR        Coul-14          LJ-14
> Protein-Protein   -8.09188e+03   -3.07618e+03    2.00961e+04    1.55028e+03
>     Protein-LIG   -9.46680e+01    5.65296e+00    0.00000e+00    0.00000e+00
>    Protein-rest   -8.75772e+03   -1.15608e+03    0.00000e+00    0.00000e+00
>         LIG-LIG    2.51151e+00   -6.58865e+00   -3.84257e+02    1.09372e+01
>        LIG-rest   -5.16843e+02   -3.54080e+01    0.00000e+00    0.00000e+00
>       rest-rest   -4.08064e+05    5.81062e+04    0.00000e+00    0.00000e+00
>   T-Protein_LIGT-Water_and_ions
>     2.99468e+02    3.00058e+02
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
> --
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