[gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?
Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule AcO starting from a structure in which they are non-covalently interacting. I'm using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection that the molecules are interacting with each other, i.e. they didn't separate during the simulation. Additionally, I've specified the energy groups aco_1, aco_2, SOL, Ion in the original MD tpr. The problem is that g_energy reports all aco_1-aco_2 energy terms as exactly 0.00. The energy terms are OK. This was only an example. I actually simulated 2, 3 and 4 copies of interacting molecules in different ways and this happens in all cases. These results were obtained using GPUs. I used the same .tpr to rerun the .xtc on CPUs only and now the aco_1-aco_2 energy terms are OK. In both cases I used GROMACS 4.6.6. I've searched the list but found nothing. Is this a problem/bug? Am I doing something wrong with the GPUs? Thank you in advance, Leandro -- 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] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?
On 9/9/14 9:09 PM, Leandro Bortot wrote: Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule AcO starting from a structure in which they are non-covalently interacting. I'm using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection that the molecules are interacting with each other, i.e. they didn't separate during the simulation. Additionally, I've specified the energy groups aco_1, aco_2, SOL, Ion in the original MD tpr. The problem is that g_energy reports all aco_1-aco_2 energy terms as exactly 0.00. The energy terms are OK. This was only an example. I actually simulated 2, 3 and 4 copies of interacting molecules in different ways and this happens in all cases. These results were obtained using GPUs. I used the same .tpr to rerun the .xtc on CPUs only and now the aco_1-aco_2 energy terms are OK. In both cases I used GROMACS 4.6.6. I've searched the list but found nothing. Is this a problem/bug? Am I doing something wrong with the GPUs? Multiple energygrps are not supported on GPU. This should be disabled in 5.0.1, and if not, hopefully the next release, as it is a known issue. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?
Thank you for your quick answer, Justin. I'll make new .edr files using only CPUs. Best regards, Leandro On Tue, Sep 9, 2014 at 10:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 9:09 PM, Leandro Bortot wrote: Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule AcO starting from a structure in which they are non-covalently interacting. I'm using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection that the molecules are interacting with each other, i.e. they didn't separate during the simulation. Additionally, I've specified the energy groups aco_1, aco_2, SOL, Ion in the original MD tpr. The problem is that g_energy reports all aco_1-aco_2 energy terms as exactly 0.00. The energy terms are OK. This was only an example. I actually simulated 2, 3 and 4 copies of interacting molecules in different ways and this happens in all cases. These results were obtained using GPUs. I used the same .tpr to rerun the .xtc on CPUs only and now the aco_1-aco_2 energy terms are OK. In both cases I used GROMACS 4.6.6. I've searched the list but found nothing. Is this a problem/bug? Am I doing something wrong with the GPUs? Multiple energygrps are not supported on GPU. This should be disabled in 5.0.1, and if not, hopefully the next release, as it is a known issue. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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.
