Re: [gmx-users] Questions regarding Polarization Energy Calculation
Hi Mark, Thanks for your reply. In the ffnonbonded.itp, I set all sigma and epsilon values to zero. So, the the LJ energy is coming as zero. But the coulomb potential is non zero. What should I do to make it zero? Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+030.0e+00 -3.47729e+04 -3.70041e+040.0e+00 Total EnergyTemperature Pressure (bar) -3.70041e+040.0e+000.0e+00 One more point: I am not sure whether getting the 0 for an energy does mean that it is not being calculated at all! It seems, the energy value was calculated but the result was zero because the sigma and epsilon were zero. In that case, the time reported by the program will also include the time of the extra calculation (unless the program is smart enough to know before hand that the result is going to be zero and return from the top!). So, while comparing with other molecular dynamic packages, its not fair to report that time for gromacs which also includes non GB time (as that can make Gromacs slower than others who do not include non GB-time). Any suggestions about this? What is the fair approach for gromacs? Thanks, Jesmin On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: 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 PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+047.53917e+07 0.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+039.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+000.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+044.17621e+13 0.0e+00 Total EnergyTemperature Pressure (bar) 4.17621e+130.0e+000.0e+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 ] ; nbfunccomb-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.abra...@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.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)
Re: [gmx-users] Questions regarding Polarization Energy Calculation
On 18/08/12, *jesmin jahan * shraba...@gmail.com wrote: Hi Mark, Thanks for your reply. In the ffnonbonded.itp, I set all sigma and epsilon values to zero. So, the the LJ energy is coming as zero. But the coulomb potential is non zero. What should I do to make it zero? Each charge-charge interaction contributes both a Coulomb term and a GB polarization term. They're computed at nearly the same time, because both need the distance, so both contribute to the same timing stats. They show up in the different energy terms that you see. There's no way to separate them - and any code that can do so is probably still slower than GROMACS doing both. Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) Potential Kinetic En. -2.23121e+030.0e+00 -3.47729e+04 -3.70041e+04 0.0e+00 Total EnergyTemperature Pressure (bar) -3.70041e+040.0e+000.0e+00 One more point: I am not sure whether getting the 0 for an energy does mean that it is not being calculated at all! Most of GROMACS is supposed to avoid computing zero interactions. It's not true for the all-vs-all GB loops, which you're not using, and currently not true for bonded interactions. Since nobody seems likely would compute without LJ in a real calculation, this is not a big deal from GROMACS point of view. I'm still skeptical about what you're trying to measure. Performance of well-written code is generally not additive from its components. If you're later going to be computing on a real molecular system, you're going to have LJ and/or bonded terms, and how well the codes compute them *together with the Coulomb terms* is what you really want to measure. It's like measuring how long a top chef takes to prepare a meal, and then wondering how they manage to feed a whole restaurant on time. They do lots of time-slicing and get lots of efficiencies of scale that are not available if you're doing just one meal. It seems, the energy value was calculated but the result was zero because the sigma and epsilon were zero. In that case, the time ...or that the LJ component of the energy is always present even if there are no interactions to compute for it, which I expect is the case. reported by the program will also include the time of the extra calculation (unless the program is smart enough to know before hand that the result is going to be zero and return from the top!). IIRC neighbour searching detects there's no LJ and so doesn't trigger loops that compute LJ. So, while comparing with other molecular dynamic packages, its not fair to report that time for gromacs which also includes non GB time (as that can make Gromacs slower than others who do not include non GB-time). Any suggestions about this? What is the fair approach for gromacs? Look at the flop break-down to see if GROMACS thinks it is computing LJ any more. Or do some real timing measurements and compare before and after. Mark Thanks, Jesmin On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: 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 PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+04 7.53917e+07 0.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+03 9.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+00 0.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+04 4.17621e+13 0.0e+00 Total EnergyTemperature Pressure (bar) 4.17621e+130.0e+000.0e+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
Re: [gmx-users] Questions regarding Polarization Energy Calculation
Okay thanks. I got it. :-) Best Regards, Jesmin On Fri, Aug 17, 2012 at 11:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 18/08/12, *jesmin jahan * shraba...@gmail.com wrote: Hi Mark, Thanks for your reply. In the ffnonbonded.itp, I set all sigma and epsilon values to zero. So, the the LJ energy is coming as zero. But the coulomb potential is non zero. What should I do to make it zero? Each charge-charge interaction contributes both a Coulomb term and a GB polarization term. They're computed at nearly the same time, because both need the distance, so both contribute to the same timing stats. They show up in the different energy terms that you see. There's no way to separate them - and any code that can do so is probably still slower than GROMACS doing both. Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) Potential Kinetic En. -2.23121e+030.0e+00 -3.47729e+04 -3.70041e+04 0.0e+00 Total EnergyTemperature Pressure (bar) -3.70041e+040.0e+000.0e+00 One more point: I am not sure whether getting the 0 for an energy does mean that it is not being calculated at all! Most of GROMACS is supposed to avoid computing zero interactions. It's not true for the all-vs-all GB loops, which you're not using, and currently not true for bonded interactions. Since nobody seems likely would compute without LJ in a real calculation, this is not a big deal from GROMACS point of view. I'm still skeptical about what you're trying to measure. Performance of well-written code is generally not additive from its components. If you're later going to be computing on a real molecular system, you're going to have LJ and/or bonded terms, and how well the codes compute them *together with the Coulomb terms* is what you really want to measure. It's like measuring how long a top chef takes to prepare a meal, and then wondering how they manage to feed a whole restaurant on time. They do lots of time-slicing and get lots of efficiencies of scale that are not available if you're doing just one meal. It seems, the energy value was calculated but the result was zero because the sigma and epsilon were zero. In that case, the time ...or that the LJ component of the energy is always present even if there are no interactions to compute for it, which I expect is the case. reported by the program will also include the time of the extra calculation (unless the program is smart enough to know before hand that the result is going to be zero and return from the top!). IIRC neighbour searching detects there's no LJ and so doesn't trigger loops that compute LJ. So, while comparing with other molecular dynamic packages, its not fair to report that time for gromacs which also includes non GB time (as that can make Gromacs slower than others who do not include non GB-time). Any suggestions about this? What is the fair approach for gromacs? Look at the flop break-down to see if GROMACS thinks it is computing LJ any more. Or do some real timing measurements and compare before and after. Mark Thanks, Jesmin On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: 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 PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+04 7.53917e+07 0.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+03 9.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+00 0.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+04 4.17621e+13 0.0e+00 Total EnergyTemperature Pressure (bar)
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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 AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+042.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+00 ... Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.005711 0.274 0.2 GB Coulomb + LJ 0.416308 25.39518.5 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 80.42658.5 Born force chain rule0.439486 6.592 4.8 NS-Pairs 0.943653 19.81714.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Bonds0.003219 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-Ekin0.006358 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-CyclesSeconds % --- Domain decomp.16 10.0430.0 1.4 Comm. coord. 16 10.0030.0 0.1 Neighbor search 16 10.1030.0 3.5 Force 16 11.5300.551.5 Wait + Comm. F16 10.2640.1 8.9 Write traj. 16 10.0620.0 2.1 Update16 10.0010.0 0.0 Comm. energies16 20.9330.331.4 Rest 16 0.0310.0 1.1 --- Total 16 2.9700.9 100.0 --- 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 0.056100.0 (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. 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? 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
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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 AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+042.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+00 ... Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.005711 0.274 0.2 GB Coulomb + LJ 0.416308 25.39518.5 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 80.42658.5 Born force chain rule0.439486 6.592 4.8 NS-Pairs 0.943653 19.81714.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Bonds0.003219 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-Ekin0.006358 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-CyclesSeconds % --- Domain decomp.16 10.0430.0 1.4 Comm. coord. 16 10.0030.0 0.1 Neighbor search 16 10.1030.0 3.5 Force 16 11.5300.551.5 Wait + Comm. F16 10.2640.1 8.9 Write traj. 16 10.0620.0 2.1 Update16 10.0010.0 0.0 Comm. energies16 20.9330.331.4 Rest 16 0.0310.0 1.1 --- Total 16 2.9700.9 100.0 --- 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 0.056100.0 (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
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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 AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+042.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+00 ... Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.005711 0.274 0.2 GB Coulomb + LJ 0.416308 25.39518.5 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 80.42658.5 Born force chain rule0.439486 6.592 4.8 NS-Pairs 0.943653 19.81714.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Bonds0.003219 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-Ekin0.006358 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-CyclesSeconds % --- Domain decomp.16 10.0430.0 1.4 Comm. coord. 16 10.0030.0 0.1 Neighbor search 16 10.1030.0 3.5 Force 16 11.5300.551.5 Wait + Comm. F16 10.2640.1 8.9 Write traj. 16 10.0620.0 2.1 Update16 10.0010.0 0.0 Comm. energies16 20.9330.331.4 Rest 16 0.0310.0 1.1 --- Total 16 2.9700.9 100.0 --- 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 0.056100.0 (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
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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.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 AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+042.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+00 ... Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.005711 0.274 0.2 GB Coulomb + LJ 0.416308 25.39518.5 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 80.42658.5 Born force chain rule0.439486 6.592 4.8 NS-Pairs 0.943653 19.81714.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Bonds0.003219 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-Ekin0.006358 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-CyclesSeconds % --- Domain decomp.16 10.0430.0 1.4 Comm. coord. 16 10.0030.0 0.1 Neighbor search 16 10.1030.0 3.5 Force 16 11.5300.551.5 Wait + Comm. F16 10.2640.1 8.9 Write traj. 16 10.0620.0 2.1 Update16 10.0010.0 0.0 Comm. energies16 20.9330.331.4 Rest 16 0.0310.0 1.1 --- Total 16 2.9700.9 100.0 --- 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 0.056100.0 (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
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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 ], and run the simulation mdrun rerun. I got output something like the following: Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+047.53917e+070.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+039.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+000.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+044.17621e+130.0e+00 Total EnergyTemperature Pressure (bar) 4.17621e+130.0e+000.0e+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 ] ; nbfunccomb-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. Thanks for your help. Sincerely, Jesmin On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham mark.abra...@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.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 AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+04 2.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+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 rule0.439486 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 Bonds0.003219 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-Ekin0.006358 0.172 0.1 - Total 137.479 100.0
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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 PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+047.53917e+070.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+039.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+000.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+044.17621e+130.0e+00 Total EnergyTemperature Pressure (bar) 4.17621e+130.0e+000.0e+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 ] ; nbfunccomb-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.abra...@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.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 AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+04 2.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+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 rule0.439486 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 Bonds0.003219 0.190 0.1 Angles
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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 listgmx-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 listgmx-users@gromacs.org
[gmx-users] Questions regarding Polarization Energy Calculation
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 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. 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? I also want to be sure that it also includes Born-Radii calculation time. 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? 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? 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 :-( 5. Is there any known speedup factor of Gromacs on multicores? Thanks for your help. Best Regards, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-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
Re: [gmx-users] Questions regarding Polarization Energy Calculation
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 listgmx-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
