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

Du, Yu duyu at sioc.ac.cn
Mon Jun 4 16:52:00 CEST 2018

Hi Mark, 

Thanks for your reply. I agree with your single point energy protocol. 

But if you grasp the details of the question I posted here, you will find that I used energygrps=Protein LIG and energygrp-table=Protein LIG in .mdp file, and I used normal table6-12.xvg for the system and zero for coul in user Protein-LIG table. So I expect that the average Coul-SR of the Protein-LIG should be zero.

Because Berk said that he hasn't been in the GMX-User list already, I posted the question in GMX-developer. If my confusion gets cleared, I will CC the thread containing whole conversation to GMX-User.


-----Original Messages-----
From:"Mark Abraham" <mark.j.abraham at gmail.com>
Sent Time:2018-05-31 23:57:39 (Thursday)
To: gmx-developers at gromacs.org
Cc: GMX-developer <gromacs.org_gmx-developers at maillist.sys.kth.se>
Subject: Re: [gmx-developers] Still one question about pme-user with user potential table and energygroup


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 range.


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 "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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