[gmx-developers] Still one question about pme-user with user potential table and energygroup
Mark Abraham
mark.j.abraham at gmail.com
Mon Jun 4 17:26:20 CEST 2018
On Mon, Jun 4, 2018 at 4:52 PM Du, Yu <duyu at sioc.ac.cn> wrote:
> 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.
>
As I said last time, the SR component is not the same as the table
contribution when you are also using PME. So the expectation that the SR
component is zero for a zero table cannot be met.
Mark
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.
>
>
> Regards,
> Yu
>
> -----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
>
>
>
> Hi,
>
> 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.
>
> Mark
>
> 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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