Re: [gmx-users] required topology stuff modification for GBSA
On 06/24/2011 02:21 PM, Makoto Yoneya wrote: Dear GROMACS experts: I'd tried to use a GBSA implicit solvent function in ver. 4.5.4. I'd convinced the normal run with vacuo with simply high epsilon_r setting. After that, I'd modified the topology stuff by adding [ implicit_genborn_params ] entry and then implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 in the mdp file to try a GBSA implicit solvent run. Then I'd suffer error from grompp like as Fatal error: Cannot find length for atoms 1-3 involved in angle. Actually, there is no covalent bond between 1-3 (there is an angle with atoms 1-2-3, but these are bonded only with 1-2 and 2-3). You don't say what your force field is, but those symptoms are suggestive of a problem with CHARMM force field lacking Urey-Bradley interaction parameters for atoms 1-2-3. If so, this is not a GB problem per se. Mark I'm wondering what kinds of extra-modification in topology stuff besides adding [ implicit_genborn_params ] entry for the implicit solvent runs from the runs without it. Any info. will be welcome. Thank you for advance. Makoto Yoneya, Dr. AIST, Tsukuba JAPAN http://staff.aist.go.jp/makoto-yoneya/ -- 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] Re: Box-dimensions -g_energy_output
Dear users, Any suggestions? Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- 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] Installation of gromacs-gpu on windows
Hello! I have a misunderstood about the installation of gpu-enabled gromacs under windows. I'll try to explain: in system requirements of gromacs-gpu it is wrote that Nvidia CUDA libraries have to be installed. But is it possible to do under cygwin? This quertion appears because we run gromacs under windows and so under cygwin. Is there a way to compile gromacs-gpu on cygwin? Will the binaries from gromacs-gpu page work and if so which of them to prefer to run under cygwin? Those for windows or for linux? -- Andrew Gontchar -- 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] lattice Coulomb energy between energy groups
Hi all I have set up a simulation with PBC using PME and specify an energy group enclusion involving some virtual sites and a hydrocarbon chain. i.e. hydrocarbon chain is one energy group and the virtual sites constitute the other group. Grompp generates the following warning Can not exclude the lattice Coulomb energy between energy groups I have checked the mailing list and the manual but there doesn't seem to be any concise answers. Given the fact that both groups are not charged is it O.K. to ignore this warning. Many Thanks Gavin -- 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] Re: Box-dimensions -g_energy_output
Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] lattice Coulomb energy between energy groups
Gavin Melaugh wrote: Hi all I have set up a simulation with PBC using PME and specify an energy group enclusion involving some virtual sites and a hydrocarbon chain. i.e. hydrocarbon chain is one energy group and the virtual sites constitute the other group. Grompp generates the following warning Can not exclude the lattice Coulomb energy between energy groups I have checked the mailing list and the manual but there doesn't seem to be any concise answers. Given the fact that both groups are not charged is it O.K. to ignore this warning. Probably. The warning indicates that one cannot use energygrp_excl to exclude components of the PME mesh; such exclusions only apply to short-range interactions that can be decomposed pairwise. Since the PME mesh is dependent on all the entities in the system, there is not way to simply calculate the mesh, except for some interactions between groups A and B. If there are no charges on groups A and B, you should be fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Re: Box-dimensions -g_energy_output
Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --__--__--- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Re: Box-dimensions -g_energy_output
Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.commailto: hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --**--** --- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] lattice Coulomb energy between energy groups
Hi Justin Thanks for the reply. I take it then, if I use the maxwarn option, it will still apply the exclusion for the short-range non-bonding interactions. Cheers Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all I have set up a simulation with PBC using PME and specify an energy group enclusion involving some virtual sites and a hydrocarbon chain. i.e. hydrocarbon chain is one energy group and the virtual sites constitute the other group. Grompp generates the following warning Can not exclude the lattice Coulomb energy between energy groups I have checked the mailing list and the manual but there doesn't seem to be any concise answers. Given the fact that both groups are not charged is it O.K. to ignore this warning. Probably. The warning indicates that one cannot use energygrp_excl to exclude components of the PME mesh; such exclusions only apply to short-range interactions that can be decomposed pairwise. Since the PME mesh is dependent on all the entities in the system, there is not way to simply calculate the mesh, except for some interactions between groups A and B. If there are no charges on groups A and B, you should be fine. -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] lattice Coulomb energy between energy groups
Gavin Melaugh wrote: Hi Justin Thanks for the reply. I take it then, if I use the maxwarn option, it will still apply the exclusion for the short-range non-bonding interactions. Yes, that should work. The error message is only there to prevent people from erroneously thinking they can exclude the PME mesh term. -Justin Cheers Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all I have set up a simulation with PBC using PME and specify an energy group enclusion involving some virtual sites and a hydrocarbon chain. i.e. hydrocarbon chain is one energy group and the virtual sites constitute the other group. Grompp generates the following warning Can not exclude the lattice Coulomb energy between energy groups I have checked the mailing list and the manual but there doesn't seem to be any concise answers. Given the fact that both groups are not charged is it O.K. to ignore this warning. Probably. The warning indicates that one cannot use energygrp_excl to exclude components of the PME mesh; such exclusions only apply to short-range interactions that can be decomposed pairwise. Since the PME mesh is dependent on all the entities in the system, there is not way to simply calculate the mesh, except for some interactions between groups A and B. If there are no charges on groups A and B, you should be fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Re: Box-dimensions -g_energy_output
Sir, I tried it already but It was huge file. this kind of nan comes only for RMSD not for any other term. I will try looking into that file again. Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --** __**--__--- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== --
Re: [gmx-users] Re: Box-dimensions -g_energy_output
Kavyashree M wrote: Sir, I tried it already but It was huge file. this kind of nan comes only for RMSD not for any other term. I will try looking into that file again. Let's keep on topic and focus on the box vectors; changing the subject midway makes it harder to arrive at a solution. The only diagnostic I can suggest is gmxdump. It should be rather obvious what's going on - your reported averages are 0.04, but the actual values from the plot are clearly different. -Justin Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --__--__--- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users
Re: [gmx-users] Re: Box-dimensions -g_energy_output
Sir, I went through the whole .edr file for one specific term in which I was getting nan. Of the three columns (Energy; Av. Energy; Sum Energy) order (power) for temperature did not change at all in the first column but in the second column there was a change of power between +1 and +2 which was +2 in another .edr file from other simulation. ven though the second column value is arround 1--e+02 while those with +1 power is around 9.--e+01 which is quite near to 1.--e+02. But I did not find any huge changes in the temperature. Thank you With Regards M. Kavyashree On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M hmkv...@gmail.com wrote: Sir, I tried it already but It was huge file. this kind of nan comes only for RMSD not for any other term. I will try looking into that file again. Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --** __**--__--- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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
Re: [gmx-users] Re: Box-dimensions -g_energy_output
Kavyashree M wrote: Sir, I went through the whole .edr file for one specific term in which I was getting nan. Of the three columns (Energy; Av. Energy; Sum Energy) order (power) for temperature did not change at all in the first column but in the second column there was a change of power between +1 and +2 which was +2 in another .edr file from other simulation. ven though the second column value is arround 1--e+02 while those with +1 power is around 9.--e+01 which is quite near to 1.--e+02. But I did not find any huge changes in the temperature. Per my previous message, please focus on the issue at hand. I do not recall the specifics of the issue with temperature and I'm not going to go digging through the archive for messages scattered over many days. You started this thread regarding box vectors, for which we have the data below in the thread. Please keep the discussion focused. If you jump around between ideas with somewhat abstract descriptions, no one is going to be interested in troubleshooting. If you want free help, make it easy to help you. If you have something relevant to post regarding box vectors, please do so, otherwise, if you want to investigate a different issue please give it proper context (new thread or including information from the old thread). Actual output would be useful, although I realize that may be too large of a message to send across the list, so snippets that illustrate anything useful would be appropriate. -Justin Thank you With Regards M. Kavyashree On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Sir, I tried it already but It was huge file. this kind of nan comes only for RMSD not for any other term. I will try looking into that file again. Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift
Re: [gmx-users] Re: Box-dimensions -g_energy_output
Sir, Thats right. But what I felt was, all these problems are connected. (I dont mean that temperature is connected to box dimension) Actually I was getting nan under RMSD for all the energy terms. I have checked the total energy graph also it is stable. even in case of box dimentions I checked the box dimensions for the whole trajectory for eg. Box-X most of the time has value around 9. very few times it gets a value near 8.9.. Thank you With Regards M. Kavyashree On Fri, Jun 24, 2011 at 6:18 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I tried it already but It was huge file. this kind of nan comes only for RMSD not for any other term. I will try looking into that file again. Let's keep on topic and focus on the box vectors; changing the subject midway makes it harder to arrive at a solution. The only diagnostic I can suggest is gmxdump. It should be rather obvious what's going on - your reported averages are 0.04, but the actual values from the plot are clearly different. -Justin Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD Tot-Drift --** --**--__--__--- Box-X 0.04532291.8 0.637535 -9.93022 (nm) Box-Y 0.04532291.8 0.637535 -9.93022 (nm) Box-Z 0.03204821.3 0.450805 -7.02173 (nm) but the dimensions of the box is different. plot attached. I am not able to figure out why only 1978700 data point are considered. Kindly give some suggestions. Thank you with regards M.Kavyashree -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080
Re: [gmx-users] Re: Box-dimensions -g_energy_output
Sir. I am sorry for changing the topic. It was not intentional It just came as I wanted to mention the other part of the problem that data had. I have checked the entire file of the gmxdump output of ener.edr firl for Box dimention as well as Temp. Thanks With Regards M. Kavyashree On Fri, Jun 24, 2011 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I went through the whole .edr file for one specific term in which I was getting nan. Of the three columns (Energy; Av. Energy; Sum Energy) order (power) for temperature did not change at all in the first column but in the second column there was a change of power between +1 and +2 which was +2 in another .edr file from other simulation. ven though the second column value is arround 1--e+02 while those with +1 power is around 9.--e+01 which is quite near to 1.--e+02. But I did not find any huge changes in the temperature. Per my previous message, please focus on the issue at hand. I do not recall the specifics of the issue with temperature and I'm not going to go digging through the archive for messages scattered over many days. You started this thread regarding box vectors, for which we have the data below in the thread. Please keep the discussion focused. If you jump around between ideas with somewhat abstract descriptions, no one is going to be interested in troubleshooting. If you want free help, make it easy to help you. If you have something relevant to post regarding box vectors, please do so, otherwise, if you want to investigate a different issue please give it proper context (new thread or including information from the old thread). Actual output would be useful, although I realize that may be too large of a message to send across the list, so snippets that illustrate anything useful would be appropriate. -Justin Thank you With Regards M. Kavyashree On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M hmkv...@gmail.com mailto: hmkv...@gmail.com wrote: Sir, I tried it already but It was huge file. this kind of nan comes only for RMSD not for any other term. I will try looking into that file again. Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards M. Kavyashree On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Any suggestions? You haven't provided nearly enough diagnostic information for anyone to offer you any useful help (as Mark said yesterday). For example, please provide: 1. Your exact g_energy command line 2. The output of gmxcheck for this .edr file 3. Your Gromacs version -Justin Thank you M. Kavyashree On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10.
Re: [gmx-users] Re: Box-dimensions -g_energy_output
Kavyashree M wrote: Sir. I am sorry for changing the topic. It was not intentional It just came as I wanted to mention the other part of the problem that data had. I'm trying to focus the discussion because you've presented three separate (maybe related) issues: 1. Wrong number of frames read 2. Wrong averages (in the case of box vectors) 3. Nonsensical standard deviations (in the case of temperature) I have checked the entire file of the gmxdump output of ener.edr firl for Box dimention as well as Temp. If there's nothing suspicious, then try processing the file with g_energy from 4.5.4; if that gives the same problem then we can rule out g_energy being at fault and the problem lies with the .edr file. But if you're saying that everything is fine, then there's no clear solution. If I recall, you've said other simulations you've done have given normal results. In that case, re-run the simulation that's causing problems (or at least a short part of it, to test) and see if you get usable output. -Justin Thanks With Regards M. Kavyashree On Fri, Jun 24, 2011 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I went through the whole .edr file for one specific term in which I was getting nan. Of the three columns (Energy; Av. Energy; Sum Energy) order (power) for temperature did not change at all in the first column but in the second column there was a change of power between +1 and +2 which was +2 in another .edr file from other simulation. ven though the second column value is arround 1--e+02 while those with +1 power is around 9.--e+01 which is quite near to 1.--e+02. But I did not find any huge changes in the temperature. Per my previous message, please focus on the issue at hand. I do not recall the specifics of the issue with temperature and I'm not going to go digging through the archive for messages scattered over many days. You started this thread regarding box vectors, for which we have the data below in the thread. Please keep the discussion focused. If you jump around between ideas with somewhat abstract descriptions, no one is going to be interested in troubleshooting. If you want free help, make it easy to help you. If you have something relevant to post regarding box vectors, please do so, otherwise, if you want to investigate a different issue please give it proper context (new thread or including information from the old thread). Actual output would be useful, although I realize that may be too large of a message to send across the list, so snippets that illustrate anything useful would be appropriate. -Justin Thank you With Regards M. Kavyashree On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Sir, I tried it already but It was huge file. this kind of nan comes only for RMSD not for any other term. I will try looking into that file again. Thanks With regards M. Kavyashree On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Sir, I am sorry I did not get any mail for that query since I posted it. So I had to ask once again.. 1. g_energy -f ener.edr -o box.xvg selecting 15 16 17 0 2. gmxcheck -e ener.edr Opened ener.edr as single precision energy file frame: 0 (index 0), t: 0.000 Last energy frame read 5 time 10.000 Found 50001 frames with a timestep of 2 ps. 3. Gromacs version 4.5.3 This is the same data where I was mentioning that I was getting not a number (nan) error for all energy calculations under RMSD section. I've said several times before that this energy file is probably junk, and again I'd suspect that. The only thing to check would be to run gmxdump on the .edr file (and redirect into some output file or pipe the output through more to actually see it) and see where the energy values go screwy. If you find a bunch of nonsensical information, then you have your answer. -Justin Thank you fro answering. With Regards
Re: [gmx-users] cross correlations
Hello, I have some doubts regarding the output file correl.dat as it contains 3 columns, but I am not able to get what are these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map... For e.g in this form Res1 Res2 Correlation coefficient x yz On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar tsje...@gmail.com wrote: Of course you did... Though mind the brackets :) C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) The point I want to make is that you can easily take the output from g_covar -ascii and turn it into a correlation matrix. In R (r-project.org) there is even a dedicated function for it: x - scan(covar.dat) x - matrix(x,sqrt(length(x))) y - cov2cor(x) write(y,correl.dat,ncolumns=3) Cheers, Tsjerk On Sun, Jun 19, 2011 at 12:37 PM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi, Thats actualy that i did here [1]. Extracting coordinate for every atom in interesting two group and computing C_ij = x_i * x_j / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is vectors [1] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret. There is another way, besides using an external tool. Extract the diagonal elements and take the square root of each. Then for each element [i,j] in the matrix, divide by the elements i and j of these square roots, and you'll have yourself a correlation matrix. Hope it helps, Tsjerk On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov ale...@omrb.pnpi.spb.ru wrote: Hi. There is two possibilitys 1. utility written by Oliver F. Lange and Helmut Grubmüller [1] that compites general corelation coefficients 2. My utility that computes pearson correlation coefficients [2] [1] http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html [2] http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote: Dear all, Is there any built in function that gives me the pairwise correlation of the fluctuation (unit vector between two coordinates of a residue) of residues (averaged over the input trajectory). I tried g_covar but thats not what im looking for. The result I want should be an NxN matrix with values ranging from -1 to 1. Thanks in advance, Nihal -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu [1] Links: -- [1] mailto:kork...@wisc.edu -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing
[gmx-users] Regarding g_dist -dist option
Hello, I just want to ask that in g_dist module, -dist option expect distance as a real argument, so the distance should be in nm or A for that... -- --- *Regards,* Bipin Singh -- 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] Regarding g_dist -dist option
bipin singh wrote: Hello, I just want to ask that in g_dist module, -dist option expect distance as a real argument, so the distance should be in nm or A for that... Please read the manual, Chapter 2. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Regarding g_dist -dist option
On Fri, Jun 24, 2011 at 10:45 AM, bipin singh bipinel...@gmail.com wrote: Hello, I just want to ask that in g_dist module, -dist option expect distance as a real argument, so the distance should be in nm or A for that... -nanometer (nm) -- --- *Regards,* Bipin Singh -- 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] pulling code
Dear Adam: I have a number of questions listed below. But first, I think it would be useful if you explain exactly what you want to accomplish and how you tried to do this with non-modified code and what problem you ran into that caused you to modify the code. After you outline that, please address the following questions: 1. Why not use one terminus as the reference group and the other terminus as the pull_group0 ? 2. How did you modify the code to use the shortest vector? I was under the impression that the code did already do this (shortest vector accounting for PBC) and that this was actually something you wanted to avoid. 3. Why can you not just use A-B even if A is positive and B is negative? If you are trying to avoid determining a PBC-wraparound distance, then it seems like A-B does give you exactly what you want as long as the entire protein is inside the unit cell. 4. If you really need to know the box size, t is available in the code at runtime. Why can you not just use the appropriate variable? 5. How are you fixing the non-terminal groups that you say need to be fixed? I don't understand why you can't fix groups with position restraints and the pull with the pull code. Also, why do you need to fix certain non-terminal groups? 6. This confused me a lot: I don't think I want to freeze or restrain the groups that need to be fixed, because they must still be allowed flexibility to twist and deform--I only want to roughly fix their centers of mass. ... so then how did you fix them? Chris. -- original message -- Hi all, I am trying to measure the energy curve of unwinding the SNARE protein complex. This requires pulling the C-termini of two helices apart from each other, while fixing certain other parts of the complex. To do this I excluded the reference group, so that all groups were pulled to absolute coordinates. However, as the protein was centered in the box, and because the box center is where the coordinates transition from -boxlength/2 to +boxlength/2 when u7. Why do you need to fix certain non-sing pbc (ie. the dateline), every time a group passes through the center of the box in any of the 3 dimensions, it is suddenly yanked violently through the box because it thinks it is now a full boxlength away from its destination. I modified the pull code to take the shortest vector between the current position and destination, which seems to fix this problem. I also modified g_wham so that it can take the difference between two groups' positions as the energy curve coordinate (since several groups need to be fixed, neither of these two groups can be used as the reference group). However, as I use pressure coupling, the box dimensions change during the simulation, and if one group has a positive and the other a negative coordinate because they straddle the center of the box, the box dimensions must be known at each timestep to get their actual separation. Is there an easier way to handle this type of simulation? I don't think I want to freeze or restrain the groups that need to be fixed, because they must still be allowed flexibility to twist and deform--I only want to roughly fix their centers of mass. Any suggestions would be appreciated, Thanks, Adam -- 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] Regarding g_dist -dist option
Thanks... On Fri, Jun 24, 2011 at 20:17, shivangi nangia shivangi.nan...@gmail.comwrote: On Fri, Jun 24, 2011 at 10:45 AM, bipin singh bipinel...@gmail.comwrote: Hello, I just want to ask that in g_dist module, -dist option expect distance as a real argument, so the distance should be in nm or A for that... -nanometer (nm) -- --- *Regards,* Bipin Singh -- 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 -- --- *Regards,* Bipin Singh -- 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] cross correlations
Hi Bipin, Read them in as a vector of numbers and divide them into sqrt(len(vector)) rows to get yourself a nice square correlation matrix. Cheers, Tsjerk On Jun 24, 2011 3:28 PM, bipin singh bipinel...@gmail.com wrote: Hello, I have some doubts regarding the output file correl.dat as it contains 3 columns, but I am not able to get what are these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map... For e.g in this form Res1 Res2 Correlation coefficient x yz On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar tsje...@gmail.com wrote: Of course you did.. --- *Regards,* Bipin Singh -- 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] ED - Projecting on an eigenvector
Dear user, When projection of a trajectory (50ns) on an eigen vector was visualised in pymol, there was broken chains, but when I projected the simulation (continued for 50 more ns ie., total 100ns) this broken chain was not seen why? Thanking you With Regards M. Kavyashree -- 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] ED - Projecting on an eigenvector
Did you make the molecules whole and removed jumps (in case of a multimer) prior to filtering? Cheers, Tsjerk On Jun 24, 2011 8:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear user, When projection of a trajectory (50ns) on an eigen vector was visualised in pymol, there was broken chains, but when I projected the simulation (continued for 50 more ns ie., total 100ns) this broken chain was not seen why? Thanking you With Regards M. Kavyashree -- 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] ED - Projecting on an eigenvector
I suppose you are writing a extr.pdb form g_anaeig. Try writing down extr. xtc and load it onto a pdb/gro using vmd. Then it should not be a problem. Best Wishes, Sarath Did you make the molecules whole and removed jumps (in case of a multimer) prior to filtering? Cheers, Tsjerk On Jun 24, 2011 8:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear user, When projection of a trajectory (50ns) on an eigen vector was visualised in pymol, there was broken chains, but when I projected the simulation (continued for 50 more ns ie., total 100ns) this broken chain was not seen why? Thanking you With Regards M. Kavyashree -- 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 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] required topology stuff modification for GBSA
Dear Mark: Thank you for your comment. You don't say what your force field is, but those symptoms are suggestive of a problem with CHARMM force field lacking Urey-Bradley interaction parameters for atoms 1-2-3. If so, this is not a GB problem per se. Mark Sorry for the lack of info. The force field was general AMBER and the topology file was basically generated using the utility ACPYPE. And as I wrote, I'd convinced the normal run with vacuo with simply high epsilon_r setting. The corresponding runs with implicit_solvent = NO result in no errors. Then I believe the error Fatal error: Cannot find length for atoms 1-3 involved in angle. occurs with some side-effects from the implicit solvent setting. Also I found the same error reports on the gmx-user archive (although no info. For solve it). It suggest the error would be a general one. Thanks anyway. Regards. -- 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] ED - Projecting on an eigenvector
Hello Sir, It is not a multimer sir, I was a single chain protein which was intact while submitting to MD. It has no problem when I project the 100ns trajectory on the vector but only in case of half of this time -50ns, it has problem. Thank you With Regards M.Kavyashree On Sat, Jun 25, 2011 at 1:56 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Did you make the molecules whole and removed jumps (in case of a multimer) prior to filtering? Cheers, Tsjerk On Jun 24, 2011 8:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear user, When projection of a trajectory (50ns) on an eigen vector was visualised in pymol, there was broken chains, but when I projected the simulation (continued for 50 more ns ie., total 100ns) this broken chain was not seen why? Thanking you With Regards M. Kavyashree -- 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 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] ED - Projecting on an eigenvector
Sir, Yes exactly I did the same. I will try with this option now. Thanks. With Regards M. Kavyashree On Sat, Jun 25, 2011 at 2:01 AM, Sarath Chandra Dantu dsar...@gwdg.dewrote: I suppose you are writing a extr.pdb form g_anaeig. Try writing down extr. xtc and load it onto a pdb/gro using vmd. Then it should not be a problem. Best Wishes, Sarath Did you make the molecules whole and removed jumps (in case of a multimer) prior to filtering? Cheers, Tsjerk On Jun 24, 2011 8:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear user, When projection of a trajectory (50ns) on an eigen vector was visualised in pymol, there was broken chains, but when I projected the simulation (continued for 50 more ns ie., total 100ns) this broken chain was not seen why? Thanking you With Regards M. Kavyashree -- 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 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
