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

Du, Yu duyu at sioc.ac.cn
Tue May 29 17:12:07 CEST 2018

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 "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 "The PME mesh contribution is subtracted from the user table by 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

   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

    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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