Re: [gmx-users] Energy minimization has stopped
Thanks a lot Justinn and Mark for the valuable suggestions. I will start over again by choosing a force field which is suitable for the RNA molecules. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:55 PM, Justin Lemkul wrote: > > > On 6/23/16 7:17 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >> The main aim of the study is to study the interaction between a polymer >> (chitosan) and RNA molecules by simulating them togather. I have already >> successfully simulated my polymer system using OPLS AA force field. >> >> To simulate them together I need to write the OPLS AA parameters for RNA >> molecules. I was suggested (Link Below) earlier that I can take the >> charges >> from any other forcefield. >> >> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) >> >> please enlight me where I am going wrong. >> >> > I think you misunderstood what I said in that thread. > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html > > "You should find force field parameters specifically for the base from > published literature or from another force field." > > This means: find a force field that has parametrized the species you need > and use it. This does not mean: hack together something from "any other > force field" you like and try to make it OPLS-AA. You did not say before > that you were dealing with a complex system like this. You just said your > guanine charges didn't add up. So I addressed that problem. > > Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an > invalid approach. > > Pick a force field. Use that force field. Do not try to kludge together > some hybrid entity. Force fields are designed to be internally > self-consistent. If you do not have a proper balance of interactions, you > are not doing a useful simulation. You are generating random numbers. > > > -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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Energy minimization has stopped
On 6/23/16 7:17 AM, Anurag Dobhal wrote: Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together I need to write the OPLS AA parameters for RNA molecules. I was suggested (Link Below) earlier that I can take the charges from any other forcefield. (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) please enlight me where I am going wrong. I think you misunderstood what I said in that thread. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html "You should find force field parameters specifically for the base from published literature or from another force field." This means: find a force field that has parametrized the species you need and use it. This does not mean: hack together something from "any other force field" you like and try to make it OPLS-AA. You did not say before that you were dealing with a complex system like this. You just said your guanine charges didn't add up. So I addressed that problem. Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an invalid approach. Pick a force field. Use that force field. Do not try to kludge together some hybrid entity. Force fields are designed to be internally self-consistent. If you do not have a proper balance of interactions, you are not doing a useful simulation. You are generating random numbers. -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] Energy minimization has stopped
Hi, You were recommended to pick a force field, not to combine parts of force fields. Choosing to simulate your polymer OPLS/AA if you then want to combine with RNA is not a good experimental design, unless you can do the combined simulation also in OPLS/AA. I would repeat the polymer experiment in whatever forcefield is also good for the experiment with RNA. Mark On Thu, Jun 23, 2016 at 1:18 PM Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear Justin, > > The main aim of the study is to study the interaction between a polymer > (chitosan) and RNA molecules by simulating them togather. I have already > successfully simulated my polymer system using OPLS AA force field. > > To simulate them together I need to write the OPLS AA parameters for RNA > molecules. I was suggested (Link Below) earlier that I can take the charges > from any other forcefield. > > (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) > > please enlight me where I am going wrong. > > Thank You > > > > > > > > > *Anurag Dobhal* > *Graduate Student (Bioprocess Technology)* > *Institute of Chemical Technology, Mumbai* > *Contact: +91 8898486877* > > > On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul wrote: > > > > > > > On 6/23/16 7:00 AM, Anurag Dobhal wrote: > > > >> I am using OPLS AA force field. parameters (charges) for the atoms are > >> taken from the charmm27 force field. > >> > >> > > So, by using some hybridized force field, you can't successfully minimize > > a structure. That should tell you something. Why are you trying to do > > this, and what leads you to believe that some hybrid OPLS/CHARMM > > combination is even sensible? You can't just mix the charges from one > > force field with another to create some kind of Frankenforcefield. > > > > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly > > optimized for RNA simulations. > > > > -Justin > > > > > >> > >> > >> *Anurag Dobhal* > >> *Graduate Student (Bioprocess Technology)* > >> *Institute of Chemical Technology, Mumbai* > >> *Contact: +91 8898486877* > >> > >> > >> > >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: > >> > >> > >>> > >>> On 6/23/16 6:44 AM, Justin Lemkul wrote: > >>> > >>> > > On 6/23/16 6:35 AM, Anurag Dobhal wrote: > > Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA > force > > field. I have written parameters using CHARMM27 force field for RNA > > molecules. > > > > > > What does this mean? Are you using OPLS-AA or CHARMM27? > > > Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly > >>> superior for RNA. > >>> > >>> -Justin > >>> > >>> > >>> Minimising the molecule by invoking mdrun gives me the follwoing error. > >>> > > > Energy minimization has stopped, but the forces have not converged to > > the > > requested precision Fmax < 1000 (which may not be possible for your > > system). > > It stopped because the algorithm tried to make a new step whose size > > was > > too > > small, or there was no change in the energy since last step. Either > > way, > > we > > regard the minimization as converged to within the available machine > > precision, given your starting configuration and EM parameters. > > > > Double precision normally gives you higher accuracy, but this is > often > > not > > needed for preparing to run molecular dynamics. > > You might need to increase your constraint accuracy, or turn > > off constraints altogether (set constraints = none in mdp file) > > > > > > > > > - > > > > The contents of the .mdp file are the following > > > > ; 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) > > > > any suggestions ? > > > > > > > > > http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to
Re: [gmx-users] Energy minimization has stopped
Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together I need to write the OPLS AA parameters for RNA molecules. I was suggested (Link Below) earlier that I can take the charges from any other forcefield. (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) please enlight me where I am going wrong. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul wrote: > > > On 6/23/16 7:00 AM, Anurag Dobhal wrote: > >> I am using OPLS AA force field. parameters (charges) for the atoms are >> taken from the charmm27 force field. >> >> > So, by using some hybridized force field, you can't successfully minimize > a structure. That should tell you something. Why are you trying to do > this, and what leads you to believe that some hybrid OPLS/CHARMM > combination is even sensible? You can't just mix the charges from one > force field with another to create some kind of Frankenforcefield. > > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly > optimized for RNA simulations. > > -Justin > > >> >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> *Contact: +91 8898486877* >> >> >> >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/23/16 6:44 AM, Justin Lemkul wrote: >>> >>> On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force > field. I have written parameters using CHARMM27 force field for RNA > molecules. > > > What does this mean? Are you using OPLS-AA or CHARMM27? Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly >>> superior for RNA. >>> >>> -Justin >>> >>> >>> Minimising the molecule by invoking mdrun gives me the follwoing error. >>> > Energy minimization has stopped, but the forces have not converged to > the > requested precision Fmax < 1000 (which may not be possible for your > system). > It stopped because the algorithm tried to make a new step whose size > was > too > small, or there was no change in the energy since last step. Either > way, > we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often > not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > > > - > > The contents of the .mdp file are the following > > ; 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) > > any suggestions ? > > > http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -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 >>> >>>
Re: [gmx-users] Energy minimization has stopped
On 6/23/16 7:00 AM, Anurag Dobhal wrote: I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. So, by using some hybridized force field, you can't successfully minimize a structure. That should tell you something. Why are you trying to do this, and what leads you to believe that some hybrid OPLS/CHARMM combination is even sensible? You can't just mix the charges from one force field with another to create some kind of Frankenforcefield. Recent RNA force fields like CHARMM36 and recent AMBER updates are highly optimized for RNA simulations. -Justin *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: On 6/23/16 6:44 AM, Justin Lemkul wrote: On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly superior for RNA. -Justin Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; 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) any suggestions ? http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -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. -- == 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] Energy minimization has stopped
I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: > > > On 6/23/16 6:44 AM, Justin Lemkul wrote: > >> >> >> On 6/23/16 6:35 AM, Anurag Dobhal wrote: >> >>> Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force >>> field. I have written parameters using CHARMM27 force field for RNA >>> molecules. >>> >>> >> What does this mean? Are you using OPLS-AA or CHARMM27? >> >> > Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly > superior for RNA. > > -Justin > > > Minimising the molecule by invoking mdrun gives me the follwoing error. >>> >>> Energy minimization has stopped, but the forces have not converged to the >>> requested precision Fmax < 1000 (which may not be possible for your >>> system). >>> It stopped because the algorithm tried to make a new step whose size was >>> too >>> small, or there was no change in the energy since last step. Either way, >>> we >>> regard the minimization as converged to within the available machine >>> precision, given your starting configuration and EM parameters. >>> >>> Double precision normally gives you higher accuracy, but this is often >>> not >>> needed for preparing to run molecular dynamics. >>> You might need to increase your constraint accuracy, or turn >>> off constraints altogether (set constraints = none in mdp file) >>> >>> >>> - >>> >>> The contents of the .mdp file are the following >>> >>> ; 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) >>> >>> any suggestions ? >>> >>> >> >> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision >> >> >> mdrun prints which atom is feeling the maximum force, so that's a good >> place to >> start looking to see if there is an actual problem. >> >> -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. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Energy minimization has stopped
On 6/23/16 6:44 AM, Justin Lemkul wrote: On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly superior for RNA. -Justin Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; 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) any suggestions ? http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -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] Energy minimization has stopped
On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; 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) any suggestions ? http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -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.
[gmx-users] Energy minimization has stopped
Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; 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) any suggestions ? *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Energy minimization has stopped, but the forces have not converged
On 6/25/14, 10:12 AM, Iris Nira Smith wrote: Hello gromacs users, I have searched the gmx-users archive and have successfully found multiple posts that provide advice on how to troubleshoot my issue. Unfortunately, after trying multiple ways to troubleshoot as suggested by each of these posts, I am still having the same issue. I successfully mutated a residue in my .pdb file using VMD mutator and am now in the minimization phase using steepest descent step-wise energy minimization. The error I keep getting is as follows: Steepest Descents: Tolerance (Fmax) = 1.0e+04 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 5.18534e+14 Fmax= 3.39138e+04, atom= 3228^M Step=1, Dmax= 1.0e-02 nm, Epot= 5.18534e+14 Fmax= 1.18748e+04, atom= 10021^M Step=2, Dmax= 5.0e-03 nm, Epot= 5.18534e+14 Fmax= 1.73483e+04, atom= 3228^M Step=3, Dmax= 2.5e-03 nm, Epot= 5.18534e+14 Fmax= 2.44124e+04, atom= 3228^M Step=4, Dmax= 1.2e-03 nm, Epot= 5.18534e+14 Fmax= 2.88081e+04, atom= 3228^M Step=5, Dmax= 6.2e-04 nm, Epot= 5.18534e+14 Fmax= 3.12647e+04, atom= 3228^M Step=6, Dmax= 3.1e-04 nm, Epot= 5.18534e+14 Fmax= 3.25644e+04, atom= 3228^M Step=7, Dmax= 1.6e-04 nm, Epot= 5.18534e+14 Fmax= 3.32326e+04, atom= 3228^M Step=8, Dmax= 7.8e-05 nm, Epot= 5.18534e+14 Fmax= 3.35718e+04, atom= 3228^M Step=9, Dmax= 3.9e-05 nm, Epot= 5.18534e+14 Fmax= 3.37432e+04, atom= 3228^M Step= 10, Dmax= 2.0e-05 nm, Epot= 5.18534e+14 Fmax= 3.38282e+04, atom= 3228^M Step= 11, Dmax= 9.8e-06 nm, Epot= 5.18534e+14 Fmax= 3.38707e+04, atom= 3228^M Step= 12, Dmax= 4.9e-06 nm, Epot= 5.18534e+14 Fmax= 3.38920e+04, atom= 3228^M Step= 13, Dmax= 2.4e-06 nm, Epot= 5.18534e+14 Fmax= 3.39031e+04, atom= 3228^M Step= 14, Dmax= 1.2e-06 nm, Epot= 5.18534e+14 Fmax= 3.39092e+04, atom= 3228^M Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax < 1 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1. Potential Energy = 5.1853375e+14 Maximum force = 3.3913793e+04 on atom 3228 Norm of force = 6.5862207e+02 I have analyzed my .gro file for steric clashes with atom 3228 (HE2 atom on a tyrosine located 20 amino acids from c-terminal tail) and the only thing that could potentially clash with it is a hydrogen atom on a nearby water which is 1.2 Angstroms away. I first moved x-coordinate of atom 3228 by 0.1nm (or 1.0 Angstrom), but the same error occurred. I then removed that entire water molecule that was near atom 3228, re-ran the energy minimization and the same error occurred. I changed the emtol from 1,000 to 10,000 even to 100,000 and the same error occurred. I then analyzed the energy using g_energy, but the following error occurred: Look at the energy terms in the .log file. Something should stick out like a sore thumb here. --- Program g_energy, VERSION 4.6.3 Source code file: /var/tmp/packages/gromacs-4.6.3/src/gmxlib/enxio.c, line: 828 Fatal error: Energy file g36r_em2.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I finally started over and created a new configuration (.gro) file as well as a topology (.top) file, but the same error occurred. Note: I have 13 other mutant model systems that I have run minimization-equilibration successfully but this particular mutant model keeps giving me the same repeated error. The potential energy of this mutant system as well as the force on atom 3228 is rather high. Can you offer any advice or alternate suggestions to troubleshooting this error? Should I run a few steps of CG first and then SD? The fact that the energy is essentially infinite and never changes means it's an unresolvable problem. There is likely something intrinsically wrong with the coordinates or the topology. You're not missing any atoms or causing pdb2gmx to do anything strange, are you? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Fac
[gmx-users] Energy minimization has stopped, but the forces have not converged
Hello gromacs users, I have searched the gmx-users archive and have successfully found multiple posts that provide advice on how to troubleshoot my issue. Unfortunately, after trying multiple ways to troubleshoot as suggested by each of these posts, I am still having the same issue. I successfully mutated a residue in my .pdb file using VMD mutator and am now in the minimization phase using steepest descent step-wise energy minimization. The error I keep getting is as follows: Steepest Descents: Tolerance (Fmax) = 1.0e+04 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 5.18534e+14 Fmax= 3.39138e+04, atom= 3228^M Step=1, Dmax= 1.0e-02 nm, Epot= 5.18534e+14 Fmax= 1.18748e+04, atom= 10021^M Step=2, Dmax= 5.0e-03 nm, Epot= 5.18534e+14 Fmax= 1.73483e+04, atom= 3228^M Step=3, Dmax= 2.5e-03 nm, Epot= 5.18534e+14 Fmax= 2.44124e+04, atom= 3228^M Step=4, Dmax= 1.2e-03 nm, Epot= 5.18534e+14 Fmax= 2.88081e+04, atom= 3228^M Step=5, Dmax= 6.2e-04 nm, Epot= 5.18534e+14 Fmax= 3.12647e+04, atom= 3228^M Step=6, Dmax= 3.1e-04 nm, Epot= 5.18534e+14 Fmax= 3.25644e+04, atom= 3228^M Step=7, Dmax= 1.6e-04 nm, Epot= 5.18534e+14 Fmax= 3.32326e+04, atom= 3228^M Step=8, Dmax= 7.8e-05 nm, Epot= 5.18534e+14 Fmax= 3.35718e+04, atom= 3228^M Step=9, Dmax= 3.9e-05 nm, Epot= 5.18534e+14 Fmax= 3.37432e+04, atom= 3228^M Step= 10, Dmax= 2.0e-05 nm, Epot= 5.18534e+14 Fmax= 3.38282e+04, atom= 3228^M Step= 11, Dmax= 9.8e-06 nm, Epot= 5.18534e+14 Fmax= 3.38707e+04, atom= 3228^M Step= 12, Dmax= 4.9e-06 nm, Epot= 5.18534e+14 Fmax= 3.38920e+04, atom= 3228^M Step= 13, Dmax= 2.4e-06 nm, Epot= 5.18534e+14 Fmax= 3.39031e+04, atom= 3228^M Step= 14, Dmax= 1.2e-06 nm, Epot= 5.18534e+14 Fmax= 3.39092e+04, atom= 3228^M Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax < 1 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 1. Potential Energy = 5.1853375e+14 Maximum force = 3.3913793e+04 on atom 3228 Norm of force = 6.5862207e+02 I have analyzed my .gro file for steric clashes with atom 3228 (HE2 atom on a tyrosine located 20 amino acids from c-terminal tail) and the only thing that could potentially clash with it is a hydrogen atom on a nearby water which is 1.2 Angstroms away. I first moved x-coordinate of atom 3228 by 0.1nm (or 1.0 Angstrom), but the same error occurred. I then removed that entire water molecule that was near atom 3228, re-ran the energy minimization and the same error occurred. I changed the emtol from 1,000 to 10,000 even to 100,000 and the same error occurred. I then analyzed the energy using g_energy, but the following error occurred: --- Program g_energy, VERSION 4.6.3 Source code file: /var/tmp/packages/gromacs-4.6.3/src/gmxlib/enxio.c, line: 828 Fatal error: Energy file g36r_em2.edr not recognized, maybe different CPU? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I finally started over and created a new configuration (.gro) file as well as a topology (.top) file, but the same error occurred. Note: I have 13 other mutant model systems that I have run minimization-equilibration successfully but this particular mutant model keeps giving me the same repeated error. The potential energy of this mutant system as well as the force on atom 3228 is rather high. Can you offer any advice or alternate suggestions to troubleshooting this error? Should I run a few steps of CG first and then SD? Thank you in advance. Iris N. Smith, Ph.D. Candidate Briggs Computational Biochemistry/Biophysics Laboratory University of Houston A Carnegie-designated Tier One public research university Email: irisnsm...@comcast.net connormichaellogsdon.blogspot.com -- 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.
