Re: [gmx-users] mdp options in GROMACS 4.5.5
On 6/7/17 10:05 AM, Mohammad Roostaie wrote: Dear Mark, I was using version 5.1.4, but I got this error when using "gmx mdrun": tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I tried version 5.0.4, too, and I got the same error. Hence, I decided to use the 4.5.5 version which does not give me that error. If you're having a problem with a specific version, you should try something *newer* rather than significantly older. Your posts about that issue went unresolved because there's not nearly enough information about what you did to install 5.1.4 (hardware, OS, compilers, your cmake command, etc). Try with 2016.3 for something modern and actively being maintained. It's a lot more effective for the developers to troubleshoot issues with the current version than one that is not even officially supported any more. -Justin Mohammad From: Mark Abraham <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com Sent: Wednesday, 7 June 2017, 13:02:46 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5 Hi,You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-)Mark On Tue, 6 Jun 2017 17:49 João Henriques <joao.m.a.henriq...@gmail.com> wrote: Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, not the integration). /J On Tue, Jun 6, 2017 at 5:45 PM, João Henriques <joao.m.a.henriq...@gmail.com wrote: Hi! I'm not sure Verlet was already implemented in GMX 4.5.5, but check the manual for that version (or the closest one). Cheers, /J On Tue, Jun 6, 2017 at 3:27 PM, <mohammad.r0...@yahoo.com> wrote: Hi All, I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error which said that the cutoff-scheme is not recognized. what should I write instead of "cutoff-scheme" in this version? Thanks,Mohammad -- 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. -- == 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] mdp options in GROMACS 4.5.5
Dear Mark, I was using version 5.1.4, but I got this error when using "gmx mdrun": tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I tried version 5.0.4, too, and I got the same error. Hence, I decided to use the 4.5.5 version which does not give me that error. Mohammad From: Mark Abraham <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com Sent: Wednesday, 7 June 2017, 13:02:46 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5 Hi,You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-)Mark On Tue, 6 Jun 2017 17:49 João Henriques <joao.m.a.henriq...@gmail.com> wrote: Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, not the integration). /J On Tue, Jun 6, 2017 at 5:45 PM, João Henriques <joao.m.a.henriq...@gmail.com > wrote: > Hi! > > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the > manual for that version (or the closest one). > > Cheers, > > /J > > On Tue, Jun 6, 2017 at 3:27 PM, <mohammad.r0...@yahoo.com> wrote: > >> Hi All, >> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - >> used as input into grompp to generate em.tpr >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> emtol = 1000.0 ; Stop minimization when the maximum >> force < 1000.0 kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 5 ; Maximum number of (minimization) steps >> to perform >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor >> list and long range forces >> cutoff-scheme = Verlet >> ns_type = grid ; Method to determine neighbor >> list (simple, grid) >> coulombtype = PME ; Treatment of long range >> electrostatic interactions >> rcoulomb = 1.0 ; Short-range electrostatic >> cut-off >> rvdw = 1.0 ; Short-range Van der Waals >> cut-off >> pbc = xyz ; Periodic Boundary Conditions >> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error >> which said that the cutoff-scheme is not recognized. what should I write >> instead of "cutoff-scheme" in this version? >> Thanks,Mohammad >> -- >> 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. -- 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] mdp options in GROMACS 4.5.5
Hi, You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-) Mark On Tue, 6 Jun 2017 17:49 João Henriqueswrote: > Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I > mean, not the integration). > > /J > > On Tue, Jun 6, 2017 at 5:45 PM, João Henriques < > joao.m.a.henriq...@gmail.com > > wrote: > > > Hi! > > > > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the > > manual for that version (or the closest one). > > > > Cheers, > > > > /J > > > > On Tue, Jun 6, 2017 at 3:27 PM, wrote: > > > >> Hi All, > >> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - > >> used as input into grompp to generate em.tpr > >> integrator = steep ; Algorithm (steep = steepest descent > >> minimization) > >> emtol = 1000.0; Stop minimization when the maximum > >> force < 1000.0 kJ/mol/nm > >> emstep = 0.01 ; Energy step size > >> nsteps = 5 ; Maximum number of (minimization) steps > >> to perform > >> > >> ; Parameters describing how to find the neighbors of each atom and how > to > >> calculate the interactions > >> nstlist = 1 ; Frequency to update the neighbor > >> list and long range forces > >> cutoff-scheme = Verlet > >> ns_type = grid ; Method to determine neighbor > >> list (simple, grid) > >> coulombtype = PME ; Treatment of long range > >> electrostatic interactions > >> rcoulomb= 1.0 ; Short-range electrostatic > >> cut-off > >> rvdw= 1.0 ; Short-range Van der Waals > >> cut-off > >> pbc = xyz ; Periodic Boundary Conditions > >> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the > error > >> which said that the cutoff-scheme is not recognized. what should I write > >> instead of "cutoff-scheme" in this version? > >> Thanks,Mohammad > >> -- > >> 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. -- 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] mdp options in GROMACS 4.5.5
Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, not the integration). /J On Tue, Jun 6, 2017 at 5:45 PM, João Henriqueswrote: > Hi! > > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the > manual for that version (or the closest one). > > Cheers, > > /J > > On Tue, Jun 6, 2017 at 3:27 PM, wrote: > >> Hi All, >> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - >> used as input into grompp to generate em.tpr >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> emtol = 1000.0; Stop minimization when the maximum >> force < 1000.0 kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 5 ; Maximum number of (minimization) steps >> to perform >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor >> list and long range forces >> cutoff-scheme = Verlet >> ns_type = grid ; Method to determine neighbor >> list (simple, grid) >> coulombtype = PME ; Treatment of long range >> electrostatic interactions >> rcoulomb= 1.0 ; Short-range electrostatic >> cut-off >> rvdw= 1.0 ; Short-range Van der Waals >> cut-off >> pbc = xyz ; Periodic Boundary Conditions >> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error >> which said that the cutoff-scheme is not recognized. what should I write >> instead of "cutoff-scheme" in this version? >> Thanks,Mohammad >> -- >> 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.
Re: [gmx-users] mdp options in GROMACS 4.5.5
Hi! I'm not sure Verlet was already implemented in GMX 4.5.5, but check the manual for that version (or the closest one). Cheers, /J On Tue, Jun 6, 2017 at 3:27 PM,wrote: > Hi All, > I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used > as input into grompp to generate em.tpr > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0; Stop minimization when the maximum force > < 1000.0 kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps = 5 ; Maximum number of (minimization) steps > to perform > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor > list and long range forces > cutoff-scheme = Verlet > ns_type = grid ; Method to determine neighbor > list (simple, grid) > coulombtype = PME ; Treatment of long range > electrostatic interactions > rcoulomb= 1.0 ; Short-range electrostatic cut-off > rvdw= 1.0 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions > (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error > which said that the cutoff-scheme is not recognized. what should I write > instead of "cutoff-scheme" in this version? > Thanks,Mohammad > -- > 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.
[gmx-users] mdp options in GROMACS 4.5.5
Hi All, I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error which said that the cutoff-scheme is not recognized. what should I write instead of "cutoff-scheme" in this version? Thanks,Mohammad -- 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.