[gmx-users] Questions regarding Polarization Energy Calculation
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Aug 16 09:27:07 CEST 2012
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
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>>>>>
>>>>>
>>>>> --
>>>>> Jesmin Jahan Tithi
>>>>> PhD Student, CS
>>>>> Stony Brook University, NY-11790.
>>>>
>>>>
>>> --
>>> gmx-users mailing list gmx-users 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.
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