[gmx-users] Questions regarding Polarization Energy Calculation
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Aug 17 06:00:26 CEST 2012
On 17/08/2012 1:14 PM, jesmin jahan wrote:
> Hi Mark,
>
> According to your advice " remove the the bonded terms and zero the
> VDW parameters",
> I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
> ],
This only removes the "bonded" terms (in the sense of those atoms that
interact because of the presence of bonds). The VDW parameters for
non-bonded interactions are in ffnonbonded.itp for your force field. You
should probably follow the advice here
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field
to get a local copy you can change conveniently.
> and run the simulation mdrun rerun.
>
> I got output something like the following:
>
>
> Energies (kJ/mol)
> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic En.
> -2.23121e+03 7.54287e+07 -3.47729e+04 7.53917e+07 0.00000e+00
> Total Energy Temperature Pressure (bar)
> 7.53917e+07 0.00000e+00 0.00000e+00
>
> where the previous output was something like this:
>
> Energies (kJ/mol)
> Bond Angle Proper Dih. Improper Dih.GB Polarization
> 2.12480e+03 4.80088e+02 1.06648e+03 9.04861e+01 -2.23122e+03
> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Potential
> 7.05695e+02 5.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03
> Kinetic En. Total Energy Temperature Pressure (bar)
> 0.00000e+00 -1.45483e+03 0.00000e+00 0.00000e+00
>
>
>
> Energies (kJ/mol)
> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic En.
> -2.23121e+03 4.17621e+13 -3.47729e+04 4.17621e+13 0.00000e+00
> Total Energy Temperature Pressure (bar)
> 4.17621e+13 0.00000e+00 0.00000e+00
>
>
> So, you can see, although it has managed to remove some extra terms,
> the LJ and Columb potential are still there. I searched for VWD
> parameters. Although I saw various options for VWD, its not clear
> from the options, how to turn it off. Could you kindly tell me more
> clearly about it?
>
>
> I was also looking into the forcefield.itp file. I set the gen-pairs
> to no , fudgeLJ 1 and fudgeQQ to 1 which were yes, .5 and .83
> respectively originally.
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 no 1 1
>
> Please let me know how to get rid of calculation of other energies
> (LJ, Culumb and Total Potential) and how to set the parameters for
> this properly.
You can't get rid of the total. It's the total. You're trying to keep
the (GB) Coulomb.
Mark
>
> Thanks for your help.
>
> Sincerely,
> Jesmin
> On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> On 16/08/2012 5:08 PM, jesmin jahan wrote:
>>> Hi Mark,
>>>
>>> Thanks for your reply.
>>> If I open the .tpr file using notepad, it seems to be a binary file.
>>> Then, how to remove the the bonded terms and zero the VDW parameters?
>>
>> In the .top file from which you made the .tpr. (And contributing .itp files)
>> Parts of chapter 5 may help with this process.
>>
>> Mark
>>
>>
>>> I really need to compare how fast different well known package can
>>> compute GB-polarization energy and how good the energy values are?
>>> That's why time is an important factor me my experiments and I really
>>> want to measure the time for GB energy in isolation !
>>>
>>> Thanks,
>>> Jesmin
>>>> On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
>>>> wrote:
>>>>> On 16/08/2012 4:26 PM, jesmin jahan wrote:
>>>>>> Hi Mark,
>>>>>>
>>>>>> Thanks for your previous reply.
>>>>>> I tried to run single point energy simulation with some proteins.
>>>>>> I got .log files with content like this:
>>>>>>
>>>>>> Energies (kJ/mol)
>>>>>> Bond Angle Proper Dih. Improper Dih.GB
>>>>>> Polarization
>>>>>> 1.54109e+04 3.84351e+03 8.47152e+03 3.58425e+02
>>>>>> -1.69666e+04
>>>>>> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
>>>>>> Potential
>>>>>> 4.29664e+03 3.63997e+04 2.22900e+05 -5.18818e+04
>>>>>> 2.22832e+05
>>>>>> Kinetic En. Total Energy Temperature Pressure (bar)
>>>>>> 1.08443e+09 1.08465e+09 2.73602e+07 0.00000e+00
>>>>>> .......
>>>>>>
>>>>>> Computing: M-Number M-Flops %
>>>>>> Flops
>>>>>>
>>>>>> -----------------------------------------------------------------------------
>>>>>> Generalized Born Coulomb 0.005711 0.274
>>>>>> 0.2
>>>>>> GB Coulomb + LJ 0.416308 25.395
>>>>>> 18.5
>>>>>> Outer nonbonded loop 0.016367 0.164
>>>>>> 0.1
>>>>>> 1,4 nonbonded interactions 0.008410 0.757
>>>>>> 0.6
>>>>>> Born radii (HCT/OBC) 0.439486 80.426
>>>>>> 58.5
>>>>>> Born force chain rule 0.439486 6.592
>>>>>> 4.8
>>>>>> NS-Pairs 0.943653 19.817
>>>>>> 14.4
>>>>>> Reset In Box 0.003179 0.010
>>>>>> 0.0
>>>>>> CG-CoM 0.006358 0.019
>>>>>> 0.0
>>>>>> Bonds 0.003219 0.190
>>>>>> 0.1
>>>>>> Angles 0.005838 0.981
>>>>>> 0.7
>>>>>> Propers 0.011273 2.582
>>>>>> 1.9
>>>>>> Virial 0.003899 0.070
>>>>>> 0.1
>>>>>> Stop-CM 0.003179 0.032
>>>>>> 0.0
>>>>>> Calc-Ekin 0.006358 0.172
>>>>>> 0.1
>>>>>>
>>>>>> -----------------------------------------------------------------------------
>>>>>> Total 137.479
>>>>>> 100.0
>>>>>>
>>>>>> -----------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>>>>>>
>>>>>> av. #atoms communicated per step for force: 2 x 6859.0
>>>>>>
>>>>>>
>>>>>> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>>>>>>
>>>>>> Computing: Nodes Number G-Cycles Seconds %
>>>>>> -----------------------------------------------------------------------
>>>>>> Domain decomp. 16 1 0.043 0.0 1.4
>>>>>> Comm. coord. 16 1 0.003 0.0 0.1
>>>>>> Neighbor search 16 1 0.103 0.0 3.5
>>>>>> Force 16 1 1.530 0.5 51.5
>>>>>> Wait + Comm. F 16 1 0.264 0.1 8.9
>>>>>> Write traj. 16 1 0.062 0.0 2.1
>>>>>> Update 16 1 0.001 0.0 0.0
>>>>>> Comm. energies 16 2 0.933 0.3 31.4
>>>>>> Rest 16 0.031 0.0 1.1
>>>>>> -----------------------------------------------------------------------
>>>>>> Total 16 2.970 0.9 100.0
>>>>>> -----------------------------------------------------------------------
>>>>>>
>>>>>> NOTE: 31 % of the run time was spent communicating energies,
>>>>>> you might want to use the -gcom option of mdrun
>>>>>>
>>>>>>
>>>>>> Parallel run - timing based on wallclock.
>>>>>>
>>>>>> NODE (s) Real (s) (%)
>>>>>> Time: 0.056 0.056 100.0
>>>>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>>>>>> Performance: 7.497 2.442 1.535 15.637
>>>>>>
>>>>>>
>>>>>> >From the log file, it seems, the time includes the time for LJ and
>>>>>> Columb Potential Energy. But as I said before, I am only interested to
>>>>>> GB-energy times. I am doing a comparative study of GB-energy
>>>>>> performance (values vs time) for different molecular dynamic packages.
>>>>>
>>>>> Since the LJ calculation also needs the distances, GROMACS does them in
>>>>> the same loops and makes no apology for being efficient. :-) If you're
>>>>> really trying to measure the time for the GB energy in isolation, then you
>>>>> will need to construct a different model physics that lacks LJ interactions.
>>>>> Or perhaps you don't really want to measure the time for GB energy in
>>>>> isolation. Depends what you're planning on using the information for, but
>>>>> usually measuring a time representative of the calculation you plan to run
>>>>> later is a good way to avoid having to account for lots of subtleties of
>>>>> different packages.
>>>>>
>>>>>
>>>>>> That's why I was trying to deduct the time for any other extra energy
>>>>>> computation time from it.
>>>>>>
>>>>>> Can anyone tell me how to get the exact time of GB-polarization energy
>>>>>> (including Born radii) and excluding the times for any other
>>>>>> additional energy (like LJ and Columb etc) from gromacs simutation?
>>>>>
>>>>> The .tpr you use for the rerun doesn't have to be one that will produce
>>>>> a sensible model physics. If you remove the bonded terms and zero the VDW
>>>>> parameters then the only thing left to compute is the electrostatics, which
>>>>> will give you the time you seek. You'll still potentially have time spent
>>>>> doing neighbour searching, and that is something you need to consider for
>>>>> gauging relative performance of different packages. Again, the times you
>>>>> measure will not be significant unless you run for at least several minutes.
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>>> Thanks,
>>>>>> Jesmin
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Aug 14, 2012 at 10:16 AM, jesmin jahan <shraban03 at gmail.com>
>>>>>> wrote:
>>>>>>> Thanks Mark for your reply. I was trying to use Single-Point Energy
>>>>>>> Calculation as you advised in your first reply but for most of the
>>>>>>> files the simulation failed because I was using the original .pdb
>>>>>>> files in the mdrun command.
>>>>>>>
>>>>>>> Anyways. I really appreciate your help.
>>>>>>> Thanks again,
>>>>>>> Jesmin
>>>>>>>
>>>>>>> On Tue, Aug 14, 2012 at 1:26 AM, Mark Abraham
>>>>>>> <Mark.Abraham at anu.edu.au> wrote:
>>>>>>>> On 14/08/2012 7:38 AM, jesmin jahan wrote:
>>>>>>>>> Dear Gromacs Users,
>>>>>>>>>
>>>>>>>>> I have some questions regarding GB-Polarization Energy Calculation
>>>>>>>>> with Gromacs. I will be grateful if someone can help me with the
>>>>>>>>> answers.
>>>>>>>>>
>>>>>>>>> I am trying to calculate GB-Polarization energy for different
>>>>>>>>> Protein
>>>>>>>>> molecules. I am interested both in energy values with the time
>>>>>>>>> required to calculate the Born Radii and Polarization Energy.
>>>>>>>>> I am not doing any energy minimization step as the files I am using
>>>>>>>>> as
>>>>>>>>> input are already minimized.
>>>>>>>>>
>>>>>>>>> Here is the content of my mdrun.mdp file:
>>>>>>>>>
>>>>>>>>> constraints = none
>>>>>>>>> integrator = md
>>>>>>>>> pbc = no
>>>>>>>>> dt = 0.001
>>>>>>>>> nsteps = 0
>>>>>>>>> implicit_solvent = GBSA
>>>>>>>>> gb_algorithm = HCT
>>>>>>>>> sa_algorithm = None
>>>>>>>>>
>>>>>>>>> And I am using following three steps for all the .pdb files I have:
>>>>>>>>>
>>>>>>>>> let x is the name of the .pdb file.
>>>>>>>>>
>>>>>>>>> pdb2gmx -f x.pdb -ter -ignh -ff amber99sb -water none
>>>>>>>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr
>>>>>>>>> mpirun -np 8 mdrun_mpi -deffnm imd -v -g x.log
>>>>>>>>
>>>>>>>> So you're not using the advice I gave you about how to calculate
>>>>>>>> single
>>>>>>>> point energies. OK.
>>>>>>>>
>>>>>>>>
>>>>>>>>> 1 .Now the running time reported by a log file also includes other
>>>>>>>>> times. Its also not clear to me whether the time includes the time
>>>>>>>>> for
>>>>>>>>> Born Radii calculations.
>>>>>>>>
>>>>>>>> The timing breakdown is printed at the end of the .log file. Likely
>>>>>>>> your
>>>>>>>> time is heavily dominated by the GB calculation and communication
>>>>>>>> cost. Born
>>>>>>>> radii calculation are part of the former, and not reported
>>>>>>>> separately. You
>>>>>>>> should not bother with timing measurements unless your run goes for
>>>>>>>> at least
>>>>>>>> several minutes, else your time will be dominated by I/O and setup
>>>>>>>> costs.
>>>>>>>>
>>>>>>>>
>>>>>>>>> So, to get the GB-energy time I am doing the following: I am also
>>>>>>>>> running a simulation with "implicit_solvent" set to "no" and I am
>>>>>>>>> taking the difference of these two (with GB and Without GB). Is that
>>>>>>>>> a
>>>>>>>>> right approach?
>>>>>>>>
>>>>>>>> No, that measures the weight difference between an apple and an
>>>>>>>> orange, not
>>>>>>>> whether the apple's seeds are heavy.
>>>>>>>>
>>>>>>>>
>>>>>>>>> I also want to be sure that it also includes Born-Radii calculation
>>>>>>>>> time.
>>>>>>>>
>>>>>>>> It's part of the GB calculation, so it's included in its timing.
>>>>>>>>
>>>>>>>>
>>>>>>>>> Is there any other approach to do this?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2. I was trying to run the simulations on 192 cores (16 nodes each
>>>>>>>>> with 12 codes). But I got "There is no domain decomposition for 12
>>>>>>>>> nodes that is compatible with the given box and a minimum cell size
>>>>>>>>> of
>>>>>>>>> 2.90226 nm" error for some pdb files. Can anyone explain what is
>>>>>>>>> happening. Is there any restriction on number of nodes can be used?
>>>>>>>>
>>>>>>>> Yes. See discussion linked from
>>>>>>>> http://www.gromacs.org/Documentation/Errors
>>>>>>>>
>>>>>>>>
>>>>>>>>> 3. I run the simulations with 1 way 96 (8 nodes each with 12 cores).
>>>>>>>>> Its not clear to me from the log file whether Gromacs is able to
>>>>>>>>> utilize all the 92 cores. It seems, it is using only 8 nodes.
>>>>>>>>> Does Gromacs use both shared and distributed memory parallelism?
>>>>>>>>
>>>>>>>> Not at the moment. Look at the top of your .log file for clues about
>>>>>>>> what
>>>>>>>> your configuration is making available to GROMACS. It is likely that
>>>>>>>> mpirun
>>>>>>>> -np 8 makes only 8 MPI processes available to GROMACS. Using more
>>>>>>>> will
>>>>>>>> require you to use your MPI installation correctly (and we can't help
>>>>>>>> with
>>>>>>>> that).
>>>>>>>>
>>>>>>>>
>>>>>>>>> 4. In the single-point energy calculation "mdrun -s input.tpr
>>>>>>>>> -rerun configuration.pdb", is the configuration.pdb mentioned is
>>>>>>>>> the
>>>>>>>>> original pdb file used on pdb2gmx with -f option? Or its a modified
>>>>>>>>> pdb file? I am asking because if I use the original file that does
>>>>>>>>> not
>>>>>>>>> work always :-(
>>>>>>>>
>>>>>>>> It can be any configuration that matches the .top file you gave to
>>>>>>>> grompp.
>>>>>>>> That's the point - you only need one run input file to compute the
>>>>>>>> energy of
>>>>>>>> any such configuration you later want. The configuration you gave to
>>>>>>>> grompp
>>>>>>>> (or any other tool) doesn't matter.
>>>>>>>>
>>>>>>>>
>>>>>>>>> 5. Is there any known speedup factor of Gromacs on multicores?
>>>>>>>>
>>>>>>>> That depends on your simulation system, hardware, network and
>>>>>>>> algorithm.
>>>>>>>> Don't bother with fewer than hundreds of atoms per core.
>>>>>>>>
>>>>>>>> Mark
>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>> * Only plain text messages are allowed!
>>>>>>>> * Please search the archive at
>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>>>>>> interface or send it to gmx-users-request at gromacs.org.
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>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Jesmin Jahan Tithi
>>>>>>> PhD Student, CS
>>>>>>> Stony Brook University, NY-11790.
>>>>>>
>>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Only plain text messages are allowed!
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>>> interface or send it to gmx-users-request at gromacs.org.
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>>>>
>>>>
>>>>
>>>> --
>>>> Jesmin Jahan Tithi
>>>> PhD Student, CS
>>>> Stony Brook University, NY-11790.
>>>>
>>>
>>> --
>>> Jesmin Jahan Tithi
>>> PhD Student, CS
>>> Stony Brook University, NY-11790.
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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