Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values
2473.318 0.7 - Core t (s) Wall t (s)(%) Time: 143196.26017940.633 798.2 4h59:00 (ns/day)(hour/ns) Performance: 24.0790.997 Finished mdrun on node 0 Fri Apr 3 19:11:15 2015 * Best regards, Nao -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Hannes Loeffler Sent: Monday, April 27, 2015 10:48 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: gmx-us...@gromacs.org Subject: Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values On Mon, 27 Apr 2015 09:05:05 -0400 Justin Lemkul mailto:jalem...@vt.edu>> wrote: On 4/27/15 9:02 AM, Hannes Loeffler wrote: On Mon, 27 Apr 2015 07:43:51 -0400 Justin Lemkul mailto:jalem...@vt.edu>> wrote: Note that without couple-moltype, you're going to be decoupling the whole system, which is (1) not what you want for calculating solvation free energy and (2) extremely slow. There is an inherent slowdown when running the free energy code, but it should not be so large. Really? I just looked into the code yesterday and I think that if you do not set couple-moltype, none of the coupling code is ever triggered. I have only played a bit with relative free energies (Gromacs 4.6) where I think you don't need any of the couple- parameters at all. Maybe I got that backwards. For relative free energies, this is true (we're doing these now); topological differences are all that are needed. For an absolute solvation free energy, one needs couple-moltype unless the B-state (dummy) is explicitly defined in the topology, AFAIK. If there is no couple-moltype, and no B-state defined in the topology, I'm not sure what the code would even be doing, actually. I think it runs a normal MD simulation for each lambda. A quick test with a A-state only topology and no couple- parameters gives only gradients with zero value. In fact, the output file says There are 0 atoms and 0 charges for free energy perturbation Cheers, Hannes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values
shed mdrun on node 0 Fri Apr 3 19:11:15 2015 * Best regards, Nao -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Hannes Loeffler Sent: Monday, April 27, 2015 10:48 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: gmx-us...@gromacs.org Subject: Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values On Mon, 27 Apr 2015 09:05:05 -0400 Justin Lemkul mailto:jalem...@vt.edu>> wrote: > > > On 4/27/15 9:02 AM, Hannes Loeffler wrote: > > On Mon, 27 Apr 2015 07:43:51 -0400 > > Justin Lemkul mailto:jalem...@vt.edu>> wrote: > > > >> Note that without couple-moltype, you're going to be decoupling the > >> whole system, which is (1) not what you want for calculating > >> solvation free energy and (2) extremely slow. There is an inherent > >> slowdown when running the free energy code, but it should not be so > >> large. > > > > Really? I just looked into the code yesterday and I think that if > > you do not set couple-moltype, none of the coupling code is ever > > triggered. I have only played a bit with relative free energies > > (Gromacs 4.6) where I think you don't need any of the couple- > > parameters at all. > > > > Maybe I got that backwards. For relative free energies, this is true > (we're doing these now); topological differences are all that are > needed. For an absolute solvation free energy, one needs > couple-moltype unless the B-state (dummy) is explicitly defined in > the topology, AFAIK. If there is no couple-moltype, and no B-state > defined in the topology, I'm not sure what the code would even be > doing, actually. I think it runs a normal MD simulation for each lambda. A quick test with a A-state only topology and no couple- parameters gives only gradients with zero value. In fact, the output file says There are 0 atoms and 0 charges for free energy perturbation Cheers, Hannes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values
On Mon, 27 Apr 2015 09:05:05 -0400 Justin Lemkul wrote: > > > On 4/27/15 9:02 AM, Hannes Loeffler wrote: > > On Mon, 27 Apr 2015 07:43:51 -0400 > > Justin Lemkul wrote: > > > >> Note that without couple-moltype, you're going to be decoupling the > >> whole system, which is (1) not what you want for calculating > >> solvation free energy and (2) extremely slow. There is an inherent > >> slowdown when running the free energy code, but it should not be so > >> large. > > > > Really? I just looked into the code yesterday and I think that if > > you do not set couple-moltype, none of the coupling code is ever > > triggered. I have only played a bit with relative free energies > > (Gromacs 4.6) where I think you don't need any of the couple- > > parameters at all. > > > > Maybe I got that backwards. For relative free energies, this is true > (we're doing these now); topological differences are all that are > needed. For an absolute solvation free energy, one needs > couple-moltype unless the B-state (dummy) is explicitly defined in > the topology, AFAIK. If there is no couple-moltype, and no B-state > defined in the topology, I'm not sure what the code would even be > doing, actually. I think it runs a normal MD simulation for each lambda. A quick test with a A-state only topology and no couple- parameters gives only gradients with zero value. In fact, the output file says There are 0 atoms and 0 charges for free energy perturbation Cheers, Hannes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values
On 4/27/15 9:02 AM, Hannes Loeffler wrote: On Mon, 27 Apr 2015 07:43:51 -0400 Justin Lemkul wrote: Note that without couple-moltype, you're going to be decoupling the whole system, which is (1) not what you want for calculating solvation free energy and (2) extremely slow. There is an inherent slowdown when running the free energy code, but it should not be so large. Really? I just looked into the code yesterday and I think that if you do not set couple-moltype, none of the coupling code is ever triggered. I have only played a bit with relative free energies (Gromacs 4.6) where I think you don't need any of the couple- parameters at all. Maybe I got that backwards. For relative free energies, this is true (we're doing these now); topological differences are all that are needed. For an absolute solvation free energy, one needs couple-moltype unless the B-state (dummy) is explicitly defined in the topology, AFAIK. If there is no couple-moltype, and no B-state defined in the topology, I'm not sure what the code would even be doing, actually. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values
On Mon, 27 Apr 2015 07:43:51 -0400 Justin Lemkul wrote: > Note that without couple-moltype, you're going to be decoupling the > whole system, which is (1) not what you want for calculating > solvation free energy and (2) extremely slow. There is an inherent > slowdown when running the free energy code, but it should not be so > large. Really? I just looked into the code yesterday and I think that if you do not set couple-moltype, none of the coupling code is ever triggered. I have only played a bit with relative free energies (Gromacs 4.6) where I think you don't need any of the couple- parameters at all. Cheers, Hannes. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] difference of calculation time between the numbers of fep-lambdas values
On 4/27/15 1:29 AM, nao.morish...@takeda.com wrote: Dear Gromacs Users, I would appreciate you to give me any comments or hints about the question below. What makes the calculation time much longer when I calculate a solvation free energy using the mdp input1 compared to the mdp input2? Input1 Free_energy = yes Couple-lambda0= vdw-q Couple-lambda1= none Couple-intramol = no Init-lambda-state = 2 Fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Calc-lambda-neighbors = 1 Input2 Free_energy = yes Couple-lambda0= vdw-q Couple-lambda1= none Couple-intramol = no Init-lambda-state = 2 Fep-lambdas = 0.0 0.1 0.2 Calc-lambda-neighbors = 1 It takes three times longer when I write down 36 lambda values compared to 3 lambda values even if there is no difference between mdp inputs other than the value of fep-lambdas and it is a normal free energy calculation not like Hamiltonian replica exchange calculation. In the second case, you're only evaluating the Hamiltonian at the native lambda and one other value (as there is only one neighbor). In the first case, you've got two neighbors. That doesn't explain the big difference in performance. Everything else about the run is the same - hardware, number of cores, etc? Note that without couple-moltype, you're going to be decoupling the whole system, which is (1) not what you want for calculating solvation free energy and (2) extremely slow. There is an inherent slowdown when running the free energy code, but it should not be so large. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
