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?
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.abra...@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 <shraba...@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.abra...@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@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! >>>>> * Please don't post (un)subscribe requests to the list. Use the www >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> >>>> >>>> -- >>>> Jesmin Jahan Tithi >>>> PhD Student, CS >>>> Stony Brook University, NY-11790. >>> >>> >>> >> >> -- >> gmx-users mailing list gmx-users@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! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > 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@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! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
