[gmx-users] step size too small
Hi all, 1) I have embedded protein into popcbilayer 2) Energy minimisation 3) Later added ions by using genion, 4) When I am trying to run minimisation its showing following sentences Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 49 steps, but did not reach the requested Fmax 100. Potential Energy = -2.1825061e+05 Maximum force = 4.3672461e+03 on atom 7008 Norm of force = 5.5597691e+04 my .mdp file is cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 500 ; ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 nstcomm = 1.0 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 When I run minimisation before adding ions it ran fine but later not why? I have searched about solve this problem in archives list and I understood that this not an error. Can I proceed further simulations Any comments will be appreciated. Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] step size too small
Minnale, Please do read the following: http://wiki.gromacs.org/index.php/Errors This one's in there. Tsjerk On Mon, Jun 30, 2008 at 11:26 AM, minnale [EMAIL PROTECTED] wrote: Hi all, 1) I have embedded protein into popcbilayer 2) Energy minimisation 3) Later added ions by using genion, 4) When I am trying to run minimisation its showing following sentences Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 49 steps, but did not reach the requested Fmax 100. Potential Energy = -2.1825061e+05 Maximum force= 4.3672461e+03 on atom 7008 Norm of force= 5.5597691e+04 my .mdp file is cpp= /usr/bin/cpp define = -DFLEX_SPC constraints= none integrator = steep nsteps = 500 ; ; Energy minimizing stuff ; emtol = 100 emstep = 0.01 nstcomm= 1.0 ns_type= grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 When I run minimisation before adding ions it ran fine but later not why? I have searched about solve this problem in archives list and I understood that this not an error. Can I proceed further simulations Any comments will be appreciated. Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Step size too small
Thanks guys. Both Tom's and Mark's suggestions will fix the problem. The reason it did not work before now in my case, was that the molecules were almost overlying (almost same coordinates in structure file), thus the inf values I got. I created some distance between them along one axis and was able to move on with EM and simulation. Rgds John From: [EMAIL PROTECTED] Subject: Re: [gmx-users] Step size too small Date: Mon, 20 Aug 2007 10:07:09 +0200 To: gmx-users@gromacs.org 17 aug 2007 kl. 21.46 skrev TJ Piggot: Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules have been successfully minimised on their own so I would suggest that your problem is with either how you edit the .top file or the distance restraint between the molecules. For my protein that has more than one identical chains pdb2gmx does not recognise them as one if you provide different chain identifiers in the pdb file, so doing this should hopefully stop you having to edit the .top file. Yes. Just removing bonds in the top-file is not a good solution. Breaking bonds changes the electronic structure of the molecule, which in turn is represented by different atom types, so you would need to change them as well, depending on the force field. Have you tried the -nomerge option for pdb2gmx? /Erik Hope this helps Tom --On 17 August 2007 19:02 +0200 Per Larsson [EMAIL PROTECTED] wrote: Hello!Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 2C_or_no_chan ge_in_energy._Converged_to_machine_precision. 2C_but_not_to_the_requested_ precisionCheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message for EM run: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.0246325e+20 Maximum force = inf on atom 1 Norm of force = inf I would appreciate any advice on how to fix this. Rgds John __ See what you’re getting into?before you go there See it! ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Find a local pizza place, movie theater, and more….then map the best route! http://maps.live.com/default.aspx?v=2ss=yp.bars~yp.pizza~yp.movie%20theatercp=42.358996~-71.056691style=rlvl=13tilt=-90dir=0alt=-1000scene=950607encType=1FORM=MGAC01___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe
Re: [gmx-users] Step size too small
17 aug 2007 kl. 21.46 skrev TJ Piggot: Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules have been successfully minimised on their own so I would suggest that your problem is with either how you edit the .top file or the distance restraint between the molecules. For my protein that has more than one identical chains pdb2gmx does not recognise them as one if you provide different chain identifiers in the pdb file, so doing this should hopefully stop you having to edit the .top file. Yes. Just removing bonds in the top-file is not a good solution. Breaking bonds changes the electronic structure of the molecule, which in turn is represented by different atom types, so you would need to change them as well, depending on the force field. Have you tried the -nomerge option for pdb2gmx? /Erik Hope this helps Tom --On 17 August 2007 19:02 +0200 Per Larsson [EMAIL PROTECTED] wrote: Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 2C_or_no_chan ge_in_energy._Converged_to_machine_precision. 2C_but_not_to_the_requested_ precision Cheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message for EM run: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.0246325e+20 Maximum force =inf on atom 1 Norm of force =inf I would appreciate any advice on how to fix this. Rgds John __ See what you’re getting into?before you go there See it! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Step size too small
Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message for EM run: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.0246325e+20 Maximum force =inf on atom 1 Norm of force =inf I would appreciate any advice on how to fix this. Rgds John _ See what you’re getting into…before you go there http://newlivehotmail.com/?ocid=TXT_TAGHM_migration_HM_viral_preview_0507___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Step size too small
Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 2C_or_no_change_in_energy._Converged_to_machine_precision. 2C_but_not_to_the_requested_precision Cheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message for EM run: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.0246325e+20 Maximum force =inf on atom 1 Norm of force =inf I would appreciate any advice on how to fix this. Rgds John See what you’re getting into…before you go there See it! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Step size too small
Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules have been successfully minimised on their own so I would suggest that your problem is with either how you edit the .top file or the distance restraint between the molecules. For my protein that has more than one identical chains pdb2gmx does not recognise them as one if you provide different chain identifiers in the pdb file, so doing this should hopefully stop you having to edit the .top file. Hope this helps Tom --On 17 August 2007 19:02 +0200 Per Larsson [EMAIL PROTECTED] wrote: Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan ge_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_ precision Cheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message for EM run: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.0246325e+20 Maximum force = inf on atom 1 Norm of force = inf I would appreciate any advice on how to fix this. Rgds John __ See what youre getting into?before you go there See it! ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
