[gmx-users] lipid.itp file CHARMM FF
Hi all, Does anybody know where can I get the lipid.itp file defined by CHARMM ? I have the popc.itp and popc.pdb files generated by CHARMM36. But what about the lipid.itp file? Thanks for your suggestions in advance. Sincerely, Shima -- 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] lipid.itp file CHARMM FF
On 15/09/2012 9:12 PM, Shima Arasteh wrote: Hi all, Does anybody know where can I get the lipid.itp file defined by CHARMM ? I have the popc.itp and popc.pdb files generated by CHARMM36. But what about the lipid.itp file? Google knows ;-) Mark -- 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] Resuming of calculation from last *.cpt
Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where md_initial is the name of the files from the run which I want to continue. As the result this produce new files with the default names traj.trr ener.edr etc. In those files the trajectory have been calculated from the last frame of the md_initial.cpt file. So as the result I've obtain again 2 set of output files ( from old and new runs). IS it possible to continue the calculations and save output within the existing files (md_initial) without creation of new ones ? James 2012/9/13 Justin Lemkul jalem...@vt.edu: On 9/13/12 9:56 AM, James Starlight wrote: Justin, I've used grompp -f md_sd.mdp -c start.gro -t incomplete.cpt -p topol.top -o incomplete.tpr mpiexec -np 48 mdrun_mpi.openmpi -v -deffnm incomplete -append where incomplete.cpt was checkpoint from previous run and -o incomplete.tpr was the name for new trajectory (in that case its equal to the name of old trajectory ) that produce new .trr .edr and other files and back up old ( e.g crete #incomplete.trr etc) ones instead of continuation of the existing ( incomplete ) trajectory What I've done wrong? You shouldn't be invoking grompp at all. http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] Resuming of calculation from last *.cpt
On 9/15/12 10:03 AM, James Starlight wrote: Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where md_initial is the name of the files from the run which I want to continue. As the result this produce new files with the default names traj.trr ener.edr etc. In those files the trajectory have been calculated from the last frame of the md_initial.cpt file. So as the result I've obtain again 2 set of output files ( from old and new runs). IS it possible to continue the calculations and save output within the existing files (md_initial) without creation of new ones ? The names of the files produced depend on what is stored in the .cpt file. mdrun will only append to files with those names. I don't have a clear picture of what you've done so it's impossible to say whether or not this is the expected outcome, but the checkpointing feature is very robust so I suspect it is. Were all of your file names originally called md_initial? If you've re-named them, the appending will fail for that very reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Resuming of calculation from last *.cpt
Jusin, yes, the initial files were named as the md_initial the simulation was resumed correctly but all output data was saved into new set of files with the default names. In my case I want that the resummed simulation data will write to the existing (md_initial) files without creation of new trajectory and other files. James 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:03 AM, James Starlight wrote: Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where md_initial is the name of the files from the run which I want to continue. As the result this produce new files with the default names traj.trr ener.edr etc. In those files the trajectory have been calculated from the last frame of the md_initial.cpt file. So as the result I've obtain again 2 set of output files ( from old and new runs). IS it possible to continue the calculations and save output within the existing files (md_initial) without creation of new ones ? The names of the files produced depend on what is stored in the .cpt file. mdrun will only append to files with those names. I don't have a clear picture of what you've done so it's impossible to say whether or not this is the expected outcome, but the checkpointing feature is very robust so I suspect it is. Were all of your file names originally called md_initial? If you've re-named them, the appending will fail for that very reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] Resuming of calculation from last *.cpt
On 9/15/12 10:11 AM, James Starlight wrote: Jusin, yes, the initial files were named as the md_initial the simulation was resumed correctly but all output data was saved into new set of files with the default names. In my case I want that the resummed simulation data will write to the existing (md_initial) files without creation of new trajectory and other files. mdrun -cpi -append -deffnm md_initial Should do the trick. -Justin James 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:03 AM, James Starlight wrote: Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where md_initial is the name of the files from the run which I want to continue. As the result this produce new files with the default names traj.trr ener.edr etc. In those files the trajectory have been calculated from the last frame of the md_initial.cpt file. So as the result I've obtain again 2 set of output files ( from old and new runs). IS it possible to continue the calculations and save output within the existing files (md_initial) without creation of new ones ? The names of the files produced depend on what is stored in the .cpt file. mdrun will only append to files with those names. I don't have a clear picture of what you've done so it's impossible to say whether or not this is the expected outcome, but the checkpointing feature is very robust so I suspect it is. Were all of your file names originally called md_initial? If you've re-named them, the appending will fail for that very reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Resuming of calculation from last *.cpt
In that case I've obtain error Fatal error: Failed to lock: md_init.log. Already running simulation? What does it means ? the md_init.log is present in the wor dir 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:11 AM, James Starlight wrote: Jusin, yes, the initial files were named as the md_initial the simulation was resumed correctly but all output data was saved into new set of files with the default names. In my case I want that the resummed simulation data will write to the existing (md_initial) files without creation of new trajectory and other files. mdrun -cpi -append -deffnm md_initial Should do the trick. -Justin James 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:03 AM, James Starlight wrote: Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where md_initial is the name of the files from the run which I want to continue. As the result this produce new files with the default names traj.trr ener.edr etc. In those files the trajectory have been calculated from the last frame of the md_initial.cpt file. So as the result I've obtain again 2 set of output files ( from old and new runs). IS it possible to continue the calculations and save output within the existing files (md_initial) without creation of new ones ? The names of the files produced depend on what is stored in the .cpt file. mdrun will only append to files with those names. I don't have a clear picture of what you've done so it's impossible to say whether or not this is the expected outcome, but the checkpointing feature is very robust so I suspect it is. Were all of your file names originally called md_initial? If you've re-named them, the appending will fail for that very reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] Resuming of calculation from last *.cpt
On 9/15/12 10:17 AM, James Starlight wrote: In that case I've obtain error Fatal error: Failed to lock: md_init.log. Already running simulation? What does it means ? the md_init.log is present in the wor dir That means mdrun expects your files to be named md_init not md_initial as you said they were named. It seems that file naming has gotten confused somewhere along the way. You can always, of course, choose -noappend and simply concatenate later. -Justin 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:11 AM, James Starlight wrote: Jusin, yes, the initial files were named as the md_initial the simulation was resumed correctly but all output data was saved into new set of files with the default names. In my case I want that the resummed simulation data will write to the existing (md_initial) files without creation of new trajectory and other files. mdrun -cpi -append -deffnm md_initial Should do the trick. -Justin James 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:03 AM, James Starlight wrote: Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where md_initial is the name of the files from the run which I want to continue. As the result this produce new files with the default names traj.trr ener.edr etc. In those files the trajectory have been calculated from the last frame of the md_initial.cpt file. So as the result I've obtain again 2 set of output files ( from old and new runs). IS it possible to continue the calculations and save output within the existing files (md_initial) without creation of new ones ? The names of the files produced depend on what is stored in the .cpt file. mdrun will only append to files with those names. I don't have a clear picture of what you've done so it's impossible to say whether or not this is the expected outcome, but the checkpointing feature is very robust so I suspect it is. Were all of your file names originally called md_initial? If you've re-named them, the appending will fail for that very reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Resuming of calculation from last *.cpt
On 16/09/2012 12:17 AM, James Starlight wrote: In that case I've obtain error Fatal error: Failed to lock: md_init.log. Already running simulation? What does it means ? the md_init.log is present in the wor dir Appending to an old run requires that all the filenames are identical between the two runs. It looks to me like your .log file was called md_init.log originally. You can use gmxdump -cp on your checkpoint file to see what the output filenames used to be, and thus what they must now be called if you want to use appending. Mark 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:11 AM, James Starlight wrote: Jusin, yes, the initial files were named as the md_initial the simulation was resumed correctly but all output data was saved into new set of files with the default names. In my case I want that the resummed simulation data will write to the existing (md_initial) files without creation of new trajectory and other files. mdrun -cpi -append -deffnm md_initial Should do the trick. -Justin James 2012/9/15 Justin Lemkul jalem...@vt.edu: On 9/15/12 10:03 AM, James Starlight wrote: Justin, In accordance to the manual I've re-launched my simulation by the command mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial -cpi md_initial -append where md_initial is the name of the files from the run which I want to continue. As the result this produce new files with the default names traj.trr ener.edr etc. In those files the trajectory have been calculated from the last frame of the md_initial.cpt file. So as the result I've obtain again 2 set of output files ( from old and new runs). IS it possible to continue the calculations and save output within the existing files (md_initial) without creation of new ones ? The names of the files produced depend on what is stored in the .cpt file. mdrun will only append to files with those names. I don't have a clear picture of what you've done so it's impossible to say whether or not this is the expected outcome, but the checkpointing feature is very robust so I suspect it is. Were all of your file names originally called md_initial? If you've re-named them, the appending will fail for that very reason. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] About EM for Cyclic Peptide
Dear Mark Thank your excellent and patience Reply. it is very useful I Did as you Instruct in Gromacs Mailing List But when I DO Energy Minimization I have got following error Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax 1000. Potential Energy = -nan Maximum force = 1.36683186708214e+07 on atom 26 Norm of force = -nan Even I have Adjusted the Various Parameters Namely emtol and emstep still the same thing is repeated -- 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] Segmentation fault (core dumped error)
Thanks very much for much for your help. The Carbon naotube issue is solved. I still have to figure out the polymers. Thanks for the info Regards Elie Date: Fri, 14 Sep 2012 10:31:28 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Segmentation fault (core dumped error) On 9/14/12 12:19 AM, Elie M wrote: Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files of CNTs and graphene (using x2top), i have found on the internet scripts (by Andrea Minoia I guess). These constitute of adding .nt2, .rtp. and .itp files to the /Gromacs/share/Gromacs/top directory (namely ffcntoplsaa.nt2, ffcntoplsaa.rtp and ffcntoplsaa.itp) and adding a line in the FF.dat file. I have done that and tried to execute x2top and I got the error: ..Entries in elements.dat: 218Looking whether force field files existOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.rtpOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tOpening library file /cygdrive/c/Packages/gromacs/share/gromacs/top/ffcntoplsaa.n2tThere are 0 name to type translationsGenerating bonds from distances...Segmentation fault (core dumped) Can anyone please tell me the source of this error and how to fix it? x2top is telling you it found nothing in the .n2t file. Either the contents are nonexistent, formatted incorrectly, or you have a line ending issue (common with Windows OS - use dos2unix if necessary). (2) I will definitely need a top file for the polymers I will also be solvating. But I also have problems because the pdb file contains a LIG residue unrecognizable by Gromacs. I have asked this question before and I was advised to change some files accordingly but to be honest I am not really professional in that; I have asked someone who had a problem in the past but he did not know all the details because he ended up not using the modified force fields after all. Can anyone give me in details how to incorporate the residue LIG within the force field or let me know whom I can consult...A part of the pdb file with the residue LIG is: COMPNDUNNAMEDAUTHORGENERATED BY OPEN BABEL 2.3.1HETATM1 C LIG 1 1.481 -1.276 -0.621 1.00 0.00 CHETATM2 C LIG 1 2.216 -2.370 -1.040 1.00 0.00 CHETATM3 S LIG 1 3.770 -2.409 -0.306 1.00 0.00 SHETATM 4 C LIG 1 3.456 -0.998 0.609 1.00 0.00 CHETATM 5 C LIG 1 2.207 -0.479 0.313 1.00 0.00 CHETATM6 C LIG 1 5.156 0.676 1.386 1.00 0.00 CHETATM7 C LIG 1 4.423 -0.491 1.600 1.00 0.00 CHETATM8 C LIG 1 4.550 -1.119 2.847 1.00 0.00 CHETATM9 C LIG 1 5.256 -0.503 3.905 1.00 0.00 CHETATM 10 C LIG 1 6.107 0.592 3.667 1.00 0.00 CHETATM 11 C LIG 1 6.008 1.181 2.393 1.00 0.00 CHETATM 12 S LIG 1 7.457 2.548 5.198 1.00 0.00 ! SHETA TM 13 C LIG 1 7.220 0.945 4.621 1.00 0.00... You need to introduce some sensible set of parameters for it. Using a generic LIG for a polymer is unlikely to work. Consult the following: http://www.gromacs.org/Documentation/How-tos/Polymers http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 minimisation of carbon nanotubes.
Dear all, I have a small question regarding energy minimization. I am minimizing a carbon naotube in vaccuo and my (mdp )input file is: ; ; SWNT (10,0) on its own ; Elie Moujaes, SWNT+polymers project ; Energy minimization input file ; cpp =/usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 0.1 emstep = 0.03 nstcomm = 1 pbc = xyz periodic_molecules = yes ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I have put emstep very loww toa chieve accuracy.In the output i got: Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e-05 Number of steps= 2000 F-max = 3.48055e+03 on atom 799 F-Norm = 9.67779e+02 Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax 1e-05 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but did not reach the requested Fmax 1e-05.Potential Energy = 8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force = 5.4860659e+00 It seems that I have to use the double precision version but as the single precision is concerned,Is the minimization fine (as the maximum force on atom 701 is 16...)? Thanks Elie -- 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] g_nmtraj -temp
Dear gromacs users, g_nmtraj states that to make the motion clearly visible in PyMol you might want to amplify it by setting an unrealistically high temperature. What temperature values do you usually need to use? To see nice domain movements, I need to set the temperature in the range 10-50K. Are those unrealistic temperatures “normal”? Many thanks, Rui Rodrigues -- 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 minimisation of carbon nanotubes.
On 9/15/12 12:49 PM, Elie M wrote: Dear all, I have a small question regarding energy minimization. I am minimizing a carbon naotube in vaccuo and my (mdp )input file is: ; ; SWNT (10,0) on its own ; Elie Moujaes, SWNT+polymers project ; Energy minimization input file ; cpp =/usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 0.1 emstep = 0.03 nstcomm = 1 pbc = xyz periodic_molecules = yes ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I have put emstep very loww toa chieve accuracy.In the output i got: Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e-05 Number of steps= 2000 F-max = 3.48055e+03 on atom 799 F-Norm = 9.67779e+02 Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax 1e-05 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but did not reach the requested Fmax 1e-05.Potential Energy = 8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force = 5.4860659e+00 It seems that I have to use the double precision version but as the single precision is concerned,Is the minimization fine (as the maximum force on atom 701 is 16...)? The outcome seems reasonable. I doubt that any algorithm, in single or double precision, would ever reach Fmax 1e-05. Values of Fmax 10 are generally suitable for just about any purpose and Fmax 1000 will generally result in stable simulations for most systems. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] About EM for Cyclic Peptide
On 9/15/12 10:45 AM, vidhya sankar wrote: Dear Mark Thank your excellent and patience Reply. it is very useful I Did as you Instruct in Gromacs Mailing List But when I DO Energy Minimization I have got following error Steepest Descents converged to machine precision in 31 steps, but did not reach the requested Fmax 1000. Potential Energy = -nan Maximum force = 1.36683186708214e+07 on atom 26 Norm of force = -nan Even I have Adjusted the Various Parameters Namely emtol and emstep still the same thing is repeated The outcome suggests there is something catastrophically wrong with the topology such that energies are essentially infinite. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] Resuming of calculation from last *.cpt
On 9/15/12 10:33 AM, James Starlight wrote: There is no errors in the filenames In the above example init and initial names were used for simplicity :) What you accomplished was confusion. Always use real file names. If you know enough to filter information and create a false reality, you'd probably be able to solve the issue without us ;) Actually the name of the simulation was md_a2a_pope_SD so I've used mpiexec -np 48 mdrun_mpi.openmpi -v -cpi md_a2a_pope_SD -deffnm md_a2a_pope_SD -append and eror was Fatal error: Failed to lock: md_a2a_pope_SD.log. Already running simulation? from cpt file after dump output filename = md_a2a_pope_SD.log I have seen this sometimes for unknown reasons. The solution is to use -noappend and concatenate later. Using the .cpt file guarantees a faithful continuation of the job; that's what is most important. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 minimisation of carbon nanotubes.
Thank you for your reply and help. Regards Elie Date: Sat, 15 Sep 2012 13:32:06 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] energy minimisation of carbon nanotubes. On 9/15/12 12:49 PM, Elie M wrote: Dear all, I have a small question regarding energy minimization. I am minimizing a carbon naotube in vaccuo and my (mdp )input file is: ; ; SWNT (10,0) on its own ; Elie Moujaes, SWNT+polymers project ; Energy minimization input file ; cpp =/usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = cg nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 0.1 emstep = 0.03 nstcomm = 1 pbc = xyz periodic_molecules = yes ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no I have put emstep very loww toa chieve accuracy.In the output i got: Reading file SWNT-EM.tpr, VERSION 4.0.5 (single precision)Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e-05 Number of steps = 2000 F-max = 3.48055e+03 on atom 799 F-Norm = 9.67779e+02 Stepsize too small, or no change in energy.Converged to machine precision,but not to the requested precision Fmax 1e-05 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 359 steps,but did not reach the requested Fmax 1e-05.Potential Energy = 8.7646348e+03Maximum force = 1.6186214e+01 on atom 701Norm of force = 5.4860659e+00 It seems that I have to use the double precision version but as the single precision is concerned,Is the minimization fine (as the maximum force on atom 701 is 16...)? The outcome seems reasonable. I doubt that any algorithm, in single or double precision, would ever reach Fmax 1e-05. Values of Fmax 10 are generally suitable for just about any purpose and Fmax 1000 will generally result in stable simulations for most systems. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
