Re: [gmx-users] Energy minimization has stopped....
On 11/5/13 7:31 AM, Kalyanashis Jana wrote: Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. You should first do what I suggested before. The reason for a large force is either (1) bad atomic clashes that should be apparent upon visual inspection or (2) bad topology for the drug. -Justin On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul wrote: On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax < 100 (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. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax < 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Energy minimization has stopped....
Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul wrote: > > > On 11/5/13 6:28 AM, Kalyanashis Jana wrote: > >> Hi, >>Whenever I am trying to do position retrained MD run, It has been >> stopped >> at middle of the MD run. I have given the following error. Can you please >> suggest me something to resolve this error? >> Energy minimization has stopped, but the forces havenot converged to the >> requested precision Fmax < 100 (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. >> >> writing lowest energy coordinates. >> >> Steepest Descents converged to machine precision in 20514 steps, >> but did not reach the requested Fmax < 100. >> Potential Energy = -9.9811250e+06 >> Maximum force = 6.1228135e+03 on atom 15461 >> Norm of force = 1.4393512e+01 >> >> > Visualize the output, specifically near atom 15461. The forces there are > too high and cannot be resolved further. Any attempt to use these > coordinates for dynamics will probably lead to a crash. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > 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 > > == > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 > -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Energy minimization has stopped....
On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax < 100 (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. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax < 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Energy minimization has stopped....
What does your curve look like? What parameters are you using in the mdp? How big is your system and what kind of molecules are in there? Providing this kind of information would help people work out what the problem is. Then again it may be ok that the minimisation has converged without reaching the Fmax cutoff. 2 is a large number of steps. > Hi, > Whenever I am trying to do position retrained MD run, It has been > stopped > at middle of the MD run. I have given the following error. Can you please > suggest me something to resolve this error? > Energy minimization has stopped, but the forces havenot converged to the > requested precision Fmax < 100 (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. > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 20514 steps, > but did not reach the requested Fmax < 100. > Potential Energy = -9.9811250e+06 > Maximum force = 6.1228135e+03 on atom 15461 > Norm of force = 1.4393512e+01 > > gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen) > > -- > Kalyanashis Jana > email: kalyan.chem...@gmail.com > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
[gmx-users] Energy minimization has stopped....
Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax < 100 (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. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax < 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 gcq#322: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen) -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
