Re: [gmx-users] Arginine_Hydrochloride topology
I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -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 -- 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] Arginine_Hydrochloride topology
shahid nayeem wrote: I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem Treat the system like you would any other normal protein. Run pdb2gmx on a coordinate file of a single molecule and proceed with building your system, which can include replication (i.e. genconf to get multiple molecules), genbox (to add other molecules and solvent), and genion. For systems with different numbers of arginine, simply alter the corresponding line in the [molecules] directive of the topology that pdb2gmx wrote. -Justin On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read 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
[gmx-users] Re: non-neutralized system
I have asked you before to keep all discussion on the gmx-users list. Please do so. It exists so that users can ask these types of questions and that others in the community can learn and contribute. I don't understand why you're running pdb2gmx on a system that already has a topology and is fully constructed. You only ever need to run pdb2gmx once to build the initial topology. What's more, its output is not necessarily reflective of the entire system. It prints charges on a per-molecule basis. Your protein will of course always have a +1 charge, so pdb2gmx tells you that. I do not know if it will print the charges of ions that it finds, although the intended purpose of pdb2gmx is not for complex systems like this, so it may not print that information at all. The only tool designed to expand the entire system topology into a complete description is grompp. As long as it says the net charge is what you think it should be (in this case, zero), there is no problem. Charges cannot change over time; they are fixed. -Justin Zahra Kayani wrote: Dear, Dr. Lemkul I so sorry for asking my question directly with mailing, but I search a lot and did not find my answer, my question is: I work on a protein with 528 residue and total charge of (-1) in top files, so in genion for neutralizing my system I add one NA+, but when I check total charge of system in npt and md steps from their .*gro* file with pdb2gmx command (pdb2gmx -f npt.gro -o output.gro -ignh -p output.top -water spce) it was +1 and it mean that my system was not neutralized, so I want ask you, what may be happen? and what should I do for solving this problem? If you help me for solving my problem I never forget your help. -- 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
[gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'
Dear all, searching for the mentioned error message I found a bug report for mdrun. It seemed to be fixed, but in my setup it appears again and I am not sure if I could do something about it. I did not attach the tpr file since it is bounced by the mailing list and I'd like to get at least a hint without waitng for approval of the rejected mail. :) The simulation crashes with 64 CPUs after step 11237000 with the following entry in the log file: --- Program mdrun, VERSION 4.5.4 Source code file: /home/breuerss/local/src/gromacs-4.5.4/src/mdlib/domdec_top.c, line: 352 Software inconsistency error: One or more interactions were multiple assigned in the domain decompostion For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That means that the simulation already ran for some time. I could also finish some runs successfully with the very same topology but different simulation parameters. For any help or hints how I could fix it I would be grateful. Best regards Sebastian -- _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 Raum 325Room 325 D-50939 KölnD-50939 Cologne, Federal Rep. of Germany _ -- 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] Arginine_Hydrochloride topology
I tried with single Arginine molecule pdb. pdb2gmx -f arg.pdb -o arg.gro -p arg.top genconf -f arg.gro -nbox 2 2 2 -o seq.gro genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro -box 1.8 1.8 1.8 command runs but it does not add protein.pdb to the box shahid nayeem On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem Treat the system like you would any other normal protein. Run pdb2gmx on a coordinate file of a single molecule and proceed with building your system, which can include replication (i.e. genconf to get multiple molecules), genbox (to add other molecules and solvent), and genion. For systems with different numbers of arginine, simply alter the corresponding line in the [molecules] directive of the topology that pdb2gmx wrote. -Justin On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.aumailto: mark.abra...@anu.edu.**au mark.abra...@anu.edu.au wrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/**Documentation/How-tos/**Multiple_Chainshttp://www.gromacs.org/Documentation/How-tos/Multiple_Chains . Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- ==**== 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://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 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 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 -- 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 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 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 -- ==**== 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
Re: [gmx-users] Arginine_Hydrochloride topology
shahid nayeem wrote: I tried with single Arginine molecule pdb. pdb2gmx -f arg.pdb -o arg.gro -p arg.top genconf -f arg.gro -nbox 2 2 2 -o seq.gro genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro -box 1.8 1.8 1.8 command runs but it does not add protein.pdb to the box What is in protein.pdb? I don't believe genbox can handle multi-residue molecules, but I could be wrong. Or there could be insufficient space, which is quite likely. A 1.8-nm box is too small for all but the tiniest proteins. The better approach: 1. Run pdb2gmx on protein.pdb 2. Run pdb2gmx on arg.pdb, convert the .top to .itp and #include it in the .top from (1) 3. Run genbox -ci to add arg.gro molecules into the system -Justin shahid nayeem On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: I couldn't get you. Does it means that for pre-positioning say 40 molecules of Arginine do I need to create 40 pdb of different coordinate then combine it with pdb of protein and then use pdb2gmx. I want to use different number of free positively charged Arginine molecule in simulation box along with protein. shahid nayeem Treat the system like you would any other normal protein. Run pdb2gmx on a coordinate file of a single molecule and proceed with building your system, which can include replication (i.e. genconf to get multiple molecules), genbox (to add other molecules and solvent), and genion. For systems with different numbers of arginine, simply alter the corresponding line in the [molecules] directive of the topology that pdb2gmx wrote. -Justin On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.__au mailto:mark.abra...@anu.edu.au wrote: On 11/08/2011 7:24 PM, shahid nayeem wrote: Hi Justin I prepared a box of SOL and arginine Hydrochloride. But when I solvate my protein with this box now the positively charged arginine is as solvent and this causes problem in grompp. It gives error like No such Molecule types ARG etc. Solvating arginine with water and preparing a box was without error. which forcefield in gromacs has inbuilt .itp file for free amino acid which I can include in my .top file. See http://www.gromacs.org/__Documentation/How-tos/__Multiple_Chains http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. Pre-position the non-water molecules, use pdb2gmx, solvate. Mark Shahid Nayeem On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am trying to find the topology and parameterof free Arginine Hydrchloride molecule in gromacs force-field format. Developing it in Pro-Drg will not serve as I will need some other parametrization tool to check it charges. If someone can help, I will be grateful. Isn't this just a protonated arginine (normal state for neutral pH) with a chloride counterion? There's nothing special about it, just run a coordinate file through pdb2gmx with the force field of your choice. -Justin -- ==__== 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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing list gmx-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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
[gmx-users] Regarding g_sham
Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- --- 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] correction for minimum image distance violation
Dear users, I have done some 16 simulations of a protein with mutations, by keeping the distance between protein atom and the simulation box to be 1.0nm (i.e, -d option in editconf) but only in one of the simulation I found violation of minimum image distance. So Should I increase the box size only for this or should I increase for all and redo the simulations? 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
Re: [gmx-users] correction for minimum image distance violation
Kavyashree M wrote: Dear users, I have done some 16 simulations of a protein with mutations, by keeping the distance between protein atom and the simulation box to be 1.0nm (i.e, -d option in editconf) but only in one of the simulation I found violation of minimum image distance. So Should I increase the box size only for this or should I increase for all and redo the simulations? There was an extensive discussion on this topic a few months back, and I thought you had posed the original question. Transient minimum image violations (only a few frames) may not be problematic, but if they are frequent then they can negatively influence the system and you'd have to do it over with a bigger box (or one with more appropriate symmetry, like a dodecahedron, if you did not do so in the first place). -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] correction for minimum image distance violation
Sir, Yes I was the one who posted that. I understand that, I had used dodecahedron and the problem here is- since i need to compare these simulations is it ok if i increase the size of the box for only this system (which is problematic) and redo the simulation or do i need to do for all 16. I hope my i am putting the question clearly. Thank you with regards Kavya On Fri, Aug 12, 2011 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, I have done some 16 simulations of a protein with mutations, by keeping the distance between protein atom and the simulation box to be 1.0nm (i.e, -d option in editconf) but only in one of the simulation I found violation of minimum image distance. So Should I increase the box size only for this or should I increase for all and redo the simulations? There was an extensive discussion on this topic a few months back, and I thought you had posed the original question. Transient minimum image violations (only a few frames) may not be problematic, but if they are frequent then they can negatively influence the system and you'd have to do it over with a bigger box (or one with more appropriate symmetry, like a dodecahedron, if you did not do so in the first place). -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/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] correction for minimum image distance violation
On 12/08/2011 11:09 PM, Kavyashree M wrote: Sir, Yes I was the one who posted that. I understand that, I had used dodecahedron and the problem here is- since i need to compare these simulations is it ok if i increase the size of the box for only this system (which is problematic) and redo the simulation or do i need to do for all 16. I hope my i am putting the question clearly. Since the purpose is to run simulations that satisfy the minimum image convention, I would re-run only the one that violated. I would apply that lesson in subsequent choices of box size. Mark Thank you with regards Kavya On Fri, Aug 12, 2011 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, I have done some 16 simulations of a protein with mutations, by keeping the distance between protein atom and the simulation box to be 1.0nm (i.e, -d option in editconf) but only in one of the simulation I found violation of minimum image distance. So Should I increase the box size only for this or should I increase for all and redo the simulations? There was an extensive discussion on this topic a few months back, and I thought you had posed the original question. Transient minimum image violations (only a few frames) may not be problematic, but if they are frequent then they can negatively influence the system and you'd have to do it over with a bigger box (or one with more appropriate symmetry, like a dodecahedron, if you did not do so in the first place). -Justin -- 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 -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto: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] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'
On 12/08/2011 9:55 PM, Sebastian Breuers wrote: Dear all, searching for the mentioned error message I found a bug report for mdrun. It seemed to be fixed, but in my setup it appears again and I am not sure if I could do something about it. I did not attach the tpr file since it is bounced by the mailing list and I'd like to get at least a hint without waitng for approval of the rejected mail. :) The simulation crashes with 64 CPUs after step 11237000 with the following entry in the log file: --- Program mdrun, VERSION 4.5.4 Source code file: /home/breuerss/local/src/gromacs-4.5.4/src/mdlib/domdec_top.c, line: 352 Software inconsistency error: One or more interactions were multiple assigned in the domain decompostion For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That means that the simulation already ran for some time. I could also finish some runs successfully with the very same topology but different simulation parameters. For any help or hints how I could fix it I would be grateful. This one really can't be managed. If you have a checkpoint file from a time close before the crash, then it may be possible for you to reproduce the error, and so to produce a starting point just before the error. Now perhaps a developer could reproduce the error with a view to fixing it... More useful from your point of view would be restarting from that checkpoint file on a different number of processors, to try to get past the problematic point. A thorough description of your system, preparation and simulation protocol might help someone else suggest a cause, but I wouldn't hold my breath :) 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] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'
On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers breue...@uni-koeln.de wrote: Dear all, searching for the mentioned error message I found a bug report for mdrun. It seemed to be fixed, but in my setup it appears again and I am not sure if I could do something about it. I did not attach the tpr file since it is bounced by the mailing list and I'd like to get at least a hint without waitng for approval of the rejected mail. :) The simulation crashes with 64 CPUs after step 11237000 with the following entry in the log file: --- Program mdrun, VERSION 4.5.4 Source code file: /home/breuerss/local/src/gromacs-4.5.4/src/mdlib/domdec_top.c, line: 352 Software inconsistency error: One or more interactions were multiple assigned in the domain decompostion For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That means that the simulation already ran for some time. I could also finish some runs successfully with the very same topology but different simulation parameters. For any help or hints how I could fix it I would be grateful. Have you tried to re-submit it, use the -cpi state.cpt -append and see whether it can continue or not? Best regards Sebastian -- _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 Raum 325 Room 325 D-50939 Köln D-50939 Cologne, Federal Rep. of Germany _ -- gmx-users mailing list gmx-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 -- Best Regards, lina -- 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] SWM4-NDP WATER MODEL AND IONS
Dear GMX users, I am using GMX4.5.4 to simulate SWM4-NDP polarizable water model, it is OK. But when I use the ions polarizable model which is in conjuction with SWM4-NDP model, the RMS force is very large: step 16: EM did not converge in 20 iterations, RMS force 7.950 step 17: EM did not converge in 20 iterations, RMS force 61.192 step 18: EM did not converge in 20 iterations, RMS force 177.091 step 19: EM did not converge in 20 iterations, RMS force 371.756 step 20: EM did not converge in 20 iterations, RMS force 624.178 step 21: EM did not converge in 20 iterations, RMS force 849.728 step 22: EM did not converge in 20 iterations, RMS force 891.695 step 23: EM did not converge in 20 iterations, RMS force 830.527 step 24: EM did not converge in 20 iterations, RMS force 803.412 step 25: EM did not converge in 20 iterations, RMS force 882.106 step 26: EM did not converge in 20 iterations, RMS force 1031.051 step 27: EM did not converge in 20 iterations, RMS force 1339.648 step 28: EM did not converge in 20 iterations, RMS force 1727.688 step 29: EM did not converge in 20 iterations, RMS force 1750.876 step 30: EM did not converge in 20 iterations, RMS force 1445.519 step 31: EM did not converge in 20 iterations, RMS force 0.033 step 32: EM did not converge in 20 iterations, RMS force 1210.740 step 33: EM did not converge in 20 iterations, RMS force 526.515 step 34: EM did not converge in 20 iterations, RMS force 0.033 step 35: EM did not converge in 20 iterations, RMS force 0.032 step 36: EM did not converge in 20 iterations, RMS force 0.032 step 37: EM did not converge in 20 iterations, RMS force 0.033 step 38: EM did not converge in 20 iterations, RMS force 0.032 step 39: EM did not converge in 20 iterations, RMS force 0.031 step 40: EM did not converge in 20 iterations, RMS force 0.032 step 41: EM did not converge in 20 iterations, RMS force 0.032 step 42: EM did not converge in 20 iterations, RMS force 0.032 step 43: EM did not converge in 20 iterations, RMS force 0.032 step 44: EM did not converge in 20 iterations, RMS force 0.032 step 45: EM did not converge in 20 iterations, RMS force 0.032 step 46: EM did not converge in 20 iterations, RMS force 0.033 step 47: EM did not converge in 20 iterations, RMS force 0.032 step 48: EM did not converge in 20 iterations, RMS force 0.033 step 49: EM did not converge in 20 iterations, RMS force 0.032 step 50: EM did not converge in 20 iterations, RMS force 0.032 step 51: EM did not converge in 20 iterations, RMS force 0.033 step 52: EM did not converge in 20 iterations, RMS force 0.032 step 53: EM did not converge in 20 iterations, RMS force 0.033 step 54: EM did not converge in 20 iterations, RMS force 0.032 step 55: EM did not converge in 20 iterations, RMS force 0.032 step 56: EM did not converge in 20 iterations, RMS force 0.032 step 57: EM did not converge in 20 iterations, RMS force 0.032 step 58: EM did not converge in 20 iterations, RMS force 0.032 step 59: EM did not converge in 20 iterations, RMS force 0.032 step 60: EM did not converge in 20 iterations, RMS force 0.032 step 61: EM did not converge in 20 iterations, RMS force 0.032 step 62: EM did not converge in 20 iterations, RMS force 0.032 step 63: EM did not converge in 20 iterations, RMS force 2.835 step 64: EM did not converge in 20 iterations, RMS force 120.556 step 65: EM did not converge in 20 iterations, RMS force 346.147 step 66: EM did not converge in 20 iterations, RMS force 634.393 step 67: EM did not converge in 20 iterations, RMS force 904.684 step 68: EM did not converge in 20 iterations, RMS force 1133.427 step 69: EM did not converge in 20 iterations, RMS force 735.408 step 70: EM did not converge in 20 iterations, RMS force 948.153 step 71: EM did not converge in 20 iterations, RMS force 967.569 step 72: EM did not converge in 20 iterations, RMS force 630.741 step 73: EM did not converge in 20 iterations, RMS force 1035.501 step 74: EM did not converge in 20 iterations, RMS force 698.937 step 75: EM did not converge in 20 iterations, RMS force 1179.575 step 76: EM did not converge in 20 iterations, RMS force 765.233 step 77: EM did not converge in 20 iterations, RMS force 939.995 step 78: EM did not converge in 20 iterations, RMS force 131.329 step 79: EM did not converge in 20 iterations, RMS force 51.797 step 80: EM did not converge in 20 iterations, RMS force 405.775 step 81: EM did not converge in 20 iterations, RMS force 161.922 step 82: EM did not converge in 20 iterations, RMS force 565.036 step 83: EM did not converge in 20 iterations, RMS force 1014.157 step 84: EM did not converge in 20 iterations, RMS force 1136.628 step 85: EM did not converge in 20 iterations, RMS force 0.033 step 86: EM did not converge in 20 iterations, RMS force 307.819 step 87: EM did not converge in 20 iterations, RMS force 0.032 step 88: EM did not converge in 20 iterations, RMS force 52.057 step 89: EM did not converge in 20 iterations, RMS force 0.032 step 90: EM did not converge in 20
Re: [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'
Hey, thank you both for the response. I at least could restart the system. And it is running beyond the crashing point. Keep the fingers crossed. :) Kind regards Sebastian Am 12.08.2011 15:41, schrieb lina: On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers breue...@uni-koeln.de wrote: Dear all, searching for the mentioned error message I found a bug report for mdrun. It seemed to be fixed, but in my setup it appears again and I am not sure if I could do something about it. I did not attach the tpr file since it is bounced by the mailing list and I'd like to get at least a hint without waitng for approval of the rejected mail. :) The simulation crashes with 64 CPUs after step 11237000 with the following entry in the log file: --- Program mdrun, VERSION 4.5.4 Source code file: /home/breuerss/local/src/gromacs-4.5.4/src/mdlib/domdec_top.c, line: 352 Software inconsistency error: One or more interactions were multiple assigned in the domain decompostion For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- That means that the simulation already ran for some time. I could also finish some runs successfully with the very same topology but different simulation parameters. For any help or hints how I could fix it I would be grateful. Have you tried to re-submit it, use the -cpi state.cpt -append and see whether it can continue or not? Best regards Sebastian -- _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 Raum 325Room 325 D-50939 KölnD-50939 Cologne, Federal Rep. of Germany _ -- 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 -- _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 Raum 325Room 325 D-50939 KölnD-50939 Cologne, Federal Rep. of Germany _ -- 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] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'
hello Just to share information. My parallel MD run also crash (very rarely) but I can always bypass the crash point using cpt files. dawei On Fri, Aug 12, 2011 at 10:02 AM, Sebastian Breuers breue...@uni-koeln.dewrote: Hey, thank you both for the response. I at least could restart the system. And it is running beyond the crashing point. Keep the fingers crossed. :) Kind regards Sebastian Am 12.08.2011 15:41, schrieb lina: On Fri, Aug 12, 2011 at 7:55 PM, Sebastian Breuers breue...@uni-koeln.de wrote: Dear all, searching for the mentioned error message I found a bug report for mdrun. It seemed to be fixed, but in my setup it appears again and I am not sure if I could do something about it. I did not attach the tpr file since it is bounced by the mailing list and I'd like to get at least a hint without waitng for approval of the rejected mail. :) The simulation crashes with 64 CPUs after step 11237000 with the following entry in the log file: --**- Program mdrun, VERSION 4.5.4 Source code file: /home/breuerss/local/src/**gromacs-4.5.4/src/mdlib/**domdec_top.c, line: 352 Software inconsistency error: One or more interactions were multiple assigned in the domain decompostion For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- That means that the simulation already ran for some time. I could also finish some runs successfully with the very same topology but different simulation parameters. For any help or hints how I could fix it I would be grateful. Have you tried to re-submit it, use the -cpi state.cpt -append and see whether it can continue or not? Best regards Sebastian -- __**__** _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 Raum 325Room 325 D-50939 KölnD-50939 Cologne, Federal Rep. of Germany __**__** _ -- 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 -- __**__** _ Sebastian Breuers Tel: +49-221-470-4108 EMail: breue...@uni-koeln.de Universität zu Köln University of Cologne Department für Chemie Department of Chemistry Organische Chemie Organic Chemistry Greinstraße 4 Greinstraße 4 Raum 325Room 325 D-50939 KölnD-50939 Cologne, Federal Rep. of Germany __**__** _ -- 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
[gmx-users] validation of ligand parameters
Hi all, I have thought of three experimental values to validate the parameters I assigned for a oligosaccharide, namely, free enthalpy of solvation, nOe effect, and some J3-couplings. For free enthalpy of solvation, I wondered why delta G was used to indicate enthalpy? Would what be measured is just the heat, i.e., delta H ? For nOe effect, should I use g_rmsdist to calculate 1/r3 and 1/r6 averaged distances? Should I correlate these values to corresponding nOe initial build-up rate or just a normal steady-state NOE? For J-couplings, I cannot find a tool within GROMACS to do this. The command g_chi only computes NMR 3J coupling constants for amino acid backbond and sidechain atoms? Thanks for any suggestion! Yun Shi -- 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] SWM4-NDP WATER MODEL AND IONS
I am quite interested in seeing this functional in GROMACS. You appear to have been more successful than me so far. However, I believe from reading the papers that the Drude particle (OD_swm4ndp) should have a mass of 0.40 while the oxygen should have a mass of 15.59994 (the true O mass is redistributed between the Drude and the O). Further, the Drude is movable and is not a dummy. It should be tethered to the O with a 1000 kcal/mol/angstrom bond (which I do not notice in the top file). Comments? On 8/12/2011 9:56 AM, zhongjin wrote: Dear GMX users, I am using GMX4.5.4 to simulate SWM4-NDP polarizable water model, it is OK. But when I use the ions polarizable model which is in conjuction with SWM4-NDP model, the *RMS force is very large:* step 16: EM did not converge in 20 iterations, RMS force 7.950 step 17: EM did not converge in 20 iterations, RMS force 61.192 step 18: EM did not converge in 20 iterations, RMS force 177.091 step 19: EM did not converge in 20 iterations, RMS force 371.756 step 20: EM did not converge in 20 iterations, RMS force 624.178 step 21: EM did not converge in 20 iterations, RMS force 849.728 step 22: EM did not converge in 20 iterations, RMS force 891.695 step 23: EM did not converge in 20 iterations, RMS force 830.527 step 24: EM did not converge in 20 iterations, RMS force 803.412 step 25: EM did not converge in 20 iterations, RMS force 882.106 step 26: EM did not converge in 20 iterations, RMS force 1031.051 step 27: EM did not converge in 20 iterations, RMS force 1339.648 step 28: EM did not converge in 20 iterations, RMS force 1727.688 step 29: EM did not converge in 20 iterations, RMS force 1750.876 step 30: EM did not converge in 20 iterations, RMS force 1445.519 step 31: EM did not converge in 20 iterations, RMS force 0.033 step 32: EM did not converge in 20 iterations, RMS force 1210.740 step 33: EM did not converge in 20 iterations, RMS force 526.515 step 34: EM did not converge in 20 iterations, RMS force 0.033 step 35: EM did not converge in 20 iterations, RMS force 0.032 step 36: EM did not converge in 20 iterations, RMS force 0.032 step 37: EM did not converge in 20 iterations, RMS force 0.033 step 38: EM did not converge in 20 iterations, RMS force 0.032 step 39: EM did not converge in 20 iterations, RMS force 0.031 step 40: EM did not converge in 20 iterations, RMS force 0.032 step 41: EM did not converge in 20 iterations, RMS force 0.032 step 42: EM did not converge in 20 iterations, RMS force 0.032 step 43: EM did not converge in 20 iterations, RMS force 0.032 step 44: EM did not converge in 20 iterations, RMS force 0.032 step 45: EM did not converge in 20 iterations, RMS force 0.032 step 46: EM did not converge in 20 iterations, RMS force 0.033 step 47: EM did not converge in 20 iterations, RMS force 0.032 step 48: EM did not converge in 20 iterations, RMS force 0.033 step 49: EM did not converge in 20 iterations, RMS force 0.032 step 50: EM did not converge in 20 iterations, RMS force 0.032 step 51: EM did not converge in 20 iterations, RMS force 0.033 step 52: EM did not converge in 20 iterations, RMS force 0.032 step 53: EM did not converge in 20 iterations, RMS force 0.033 step 54: EM did not converge in 20 iterations, RMS force 0.032 step 55: EM did not converge in 20 iterations, RMS force 0.032 step 56: EM did not converge in 20 iterations, RMS force 0.032 step 57: EM did not converge in 20 iterations, RMS force 0.032 step 58: EM did not converge in 20 iterations, RMS force 0.032 step 59: EM did not converge in 20 iterations, RMS force 0.032 step 60: EM did not converge in 20 iterations, RMS force 0.032 step 61: EM did not converge in 20 iterations, RMS force 0.032 step 62: EM did not converge in 20 iterations, RMS force 0.032 step 63: EM did not converge in 20 iterations, RMS force 2.835 step 64: EM did not converge in 20 iterations, RMS force 120.556 step 65: EM did not converge in 20 iterations, RMS force 346.147 step 66: EM did not converge in 20 iterations, RMS force 634.393 step 67: EM did not converge in 20 iterations, RMS force 904.684 step 68: EM did not converge in 20 iterations, RMS force 1133.427 step 69: EM did not converge in 20 iterations, RMS force 735.408 step 70: EM did not converge in 20 iterations, RMS force 948.153 step 71: EM did not converge in 20 iterations, RMS force 967.569 step 72: EM did not converge in 20 iterations, RMS force 630.741 step 73: EM did not converge in 20 iterations, RMS force 1035.501 step 74: EM did not converge in 20 iterations, RMS force 698.937 step 75: EM did not converge in 20 iterations, RMS force 1179.575 step 76: EM did not converge in 20 iterations, RMS force 765.233 step 77: EM did not converge in 20 iterations, RMS force 939.995 step 78: EM did not converge in 20 iterations, RMS force 131.329 step 79: EM did not converge in 20 iterations, RMS force 51.797 step 80: EM did not converge in 20 iterations, RMS force 405.775 step 81: EM did not converge in 20 iterations, RMS force
[gmx-users] possible bug in structure factor calculation in g_rdf?
Hi, I was using gromacs 4.0.7 to calculate the scattering intensity of polymer solvated in a solvent. But, I found a discrepancy in the normalization of the calculation when considering only a subset of the entire system ( e.g . only solute from the entire solution) : This is what I found: I first tried to calculate the scattering intensity of *only* the polymer ( i.e the solute) using trajectory file of the entire solution and .tpr file of the entire solution using an index file as shown below g_rdf_4mpi -s topol -f traj -noxvgr -n -sq sq_polymer_only EOF 6 EOF ( Here index-group 6 is the entire polymer). But, then I generated a .tpr file *only* for the solute ( i.e no solvent) and used trjconv to generate the .xtc file *only* for the solute trjconv_4mpi -s topol.tpr -f traj.xtc -n index.ndx -o traj_polymer_only.xtc Now, If I try to calculate the scattering intensity, this time using newly generated .xtc file *only* containing the solute and the new .tpr file *only* containing the solute as follows: g_rdf_4mpi -s topol_polymer_only.tpr -f traj_polymer_only.xtc -noxvgr -sq sq_polymer_only1 I get much higher scattering intensity compared to the earlier case ( where trajectory of the entire solution was used and a index file was provided to consider the solute only for calculation purpose), however the peak position is same for both cases. I think, possibly, there might be a bug which does the normalization for the entire solution in stead of the subset of the system if asked to. Any help in clarifying it will be helpful. Sanku-- 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] How to suppress the screen info how to overwrite files?
Dear gromacs users, I am using gromacs 4.0.7 or higher and I would like to ask you two simple questions. For a certain purpose, I use gromacs (grompp or mdrun) many times, and the same information appear on the screen, which might make the computational process slow. How can I suppress such information on the screen? The other question is, when using gromacs many times, it writes many backup files with sharp, which would be messy or make the process slow. How can I overwrite files in gromacs? I appreciate your help in advance. -- Hiroshi Fujisaki fujis...@nms.ac.jp Department of Physics Nippon Medical School 2-297-2 Kosugi-cho, Nakahara, Kawasaki, Kanagawa 211-0063, Japan Tel: +81-44-733-3496 Fax: +81-44-722-1231 -- 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] How to suppress the screen info how to overwrite files?
Hiroshi Fujisaki wrote: Dear gromacs users, I am using gromacs 4.0.7 or higher and I would like to ask you two simple questions. For a certain purpose, I use gromacs (grompp or mdrun) many times, and the same information appear on the screen, which might make the computational process slow. How can I suppress such information on the screen? Use the -quiet option or redirect all screen output with /dev/null. The other question is, when using gromacs many times, it writes many backup files with sharp, which would be messy or make the process slow. How can I overwrite files in gromacs? Try setting the environment variable GMX_MAXBACKUP to zero. -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] How to suppress the screen info how to overwrite files?
Dear Justin, Thanks for your prompt reply and help. I understood about the first item, but even if I type export GMX_MAXBACKUP=0 (bash) it does not seem to work. What is the recommended procedure? Is there any problem with revision? I appreciate your help. Best wishes, Hiroshi Fujisaki wrote: Dear gromacs users, I am using gromacs 4.0.7 or higher and I would like to ask you two simple questions. For a certain purpose, I use gromacs (grompp or mdrun) many times, and the same information appear on the screen, which might make the computational process slow. How can I suppress such information on the screen? Use the -quiet option or redirect all screen output with /dev/null. The other question is, when using gromacs many times, it writes many backup files with sharp, which would be messy or make the process slow. How can I overwrite files in gromacs? Try setting the environment variable GMX_MAXBACKUP to zero. -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 -- Hiroshi Fujisaki fujis...@nms.ac.jp Department of Physics Nippon Medical School 2-297-2 Kosugi-cho, Nakahara, Kawasaki, Kanagawa 211-0063, Japan Tel: +81-44-733-3496 Fax: +81-44-722-1231 -- 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] How to suppress the screen info how to overwrite files?
It is possible that the terminal that used to run gromacs does not have GMX_MAXBACKUP set up. if you use some queue software, put export GMX_MAXBACKUP=0 in the submitting script or even put it into your .bashrc file. On Fri, Aug 12, 2011 at 1:53 PM, Hiroshi Fujisaki fujis...@nms.ac.jpwrote: Dear Justin, Thanks for your prompt reply and help. I understood about the first item, but even if I type export GMX_MAXBACKUP=0 (bash) it does not seem to work. What is the recommended procedure? Is there any problem with revision? I appreciate your help. Best wishes, Hiroshi Fujisaki wrote: Dear gromacs users, I am using gromacs 4.0.7 or higher and I would like to ask you two simple questions. For a certain purpose, I use gromacs (grompp or mdrun) many times, and the same information appear on the screen, which might make the computational process slow. How can I suppress such information on the screen? Use the -quiet option or redirect all screen output with /dev/null. The other question is, when using gromacs many times, it writes many backup files with sharp, which would be messy or make the process slow. How can I overwrite files in gromacs? Try setting the environment variable GMX_MAXBACKUP to zero. -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 -- Hiroshi Fujisaki fujis...@nms.ac.jp Department of Physics Nippon Medical School 2-297-2 Kosugi-cho, Nakahara, Kawasaki, Kanagawa 211-0063, Japan Tel: +81-44-733-3496 Fax: +81-44-722-1231 -- 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] Regarding mdrunfor small organic molecules
Dear All, When I try to grompp to generate .tpr file for mdrun from topology generated by prodrg I am getting the following error. Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'PRODRG' --- Program grompp_d, VERSION 4.5.4 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am herewith attaching the chlor.top file please help me findout the problem. ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; #include ffG43a1.itp [ moleculetype ] ; Name nrexcl PRODRG3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 O 1 PDB OAE 1 -0.6772 15.9994 2 C 1 PDB CAK 10.8450 12.0110 3 C 1 PDB CAG 10.0134 12.0110 4CL 1 PDBCLAA 1 -0.0968 35.4530 5 C 1 PDB CAH 20.0134 12.0110 6CL 1 PDBCLAB 2 -0.0968 35.4530 7 C 1 PDB CAL 20.8450 12.0110 8 O 1 PDB OAF 2 -0.6772 15.9994 9 C 1 PDB CAJ 20.0134 12.0110 10CL 1 PDBCLAD 2 -0.0968 35.4530 11 C 1 PDB CAI 20.0134 12.0110 12CL 1 PDBCLAC 3 -0.0968 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.123 1660.00.123 1660.0 ; CAK OAE 2 3 20.139 1080.00.139 1080.0 ; CAK CAG 2 11 20.139 1080.00.139 1080.0 ; CAK CAI 3 4 20.173 2928800.00.173 2928800.0 ; CAG CLAA 3 5 20.139 1080.00.139 1080.0 ; CAG CAH 5 6 20.173 2928800.00.173 2928800.0 ; CAH CLAB 5 7 20.139 1080.00.139 1080.0 ; CAH CAL 7 8 20.123 1660.00.123 1660.0 ; CAL OAF 7 9 20.139 1080.00.139 1080.0 ; CAL CAJ 9 10 20.173 2928800.00.173 2928800.0 ; CAJ CLAD 9 11 20.139 1080.00.139 1080.0 ; CAJ CAI 11 12 20.173 2928800.00.173 2928800.0 ; CAI CLAC [ pairs ] ; ai aj fuc0, c1, ... 1 4 1 ; OAE CLAA 1 5 1 ; OAE CAH 1 9 1 ; OAE CAJ 1 12 1 ; OAE CLAC 2 6 1 ; CAK CLAB 2 7 1 ; CAK CAL 2 10 1 ; CAK CLAD 3 8 1 ; CAG OAF 3 9 1 ; CAG CAJ 3 12 1 ; CAG CLAC 4 6 1 ; CLAA CLAB 4 7 1 ; CLAA CAL 4 11 1 ; CLAA CAI 5 10 1 ; CAH CLAD 5 11 1 ; CAH CAI 6 8 1 ; CLAB OAF 6 9 1 ; CLAB CAJ 7 12 1 ; CAL CLAC 8 10 1 ; OAF CLAD 8 11 1 ; OAF CAI 10 12 1 ; CLAD CLAC [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2121.0 685.0121.0 685.0 ; OAE CAK CAG 1 2 11 2121.0 685.0121.0 685.0 ; OAE CAK CAI 3 2 11 2120.0 560.0120.0 560.0 ; CAG CAK CAI 2 3 4 2120.0 560.0120.0 560.0 ; CAK CAG CLAA 2 3 5 2120.0 560.0120.0 560.0 ; CAK CAG CAH 4 3 5 2120.0 560.0120.0 560.0 ; CLAA CAG CAH 3 5 6 2120.0 560.0120.0 560.0 ; CAG CAH CLAB 3 5 7 2120.0 560.0120.0 560.0 ; CAG CAH CAL 6 5 7 2120.0 560.0120.0 560.0 ; CLAB CAH CAL 5 7 8 2121.0 685.0121.0 685.0 ; CAH CAL OAF 5 7 9 2120.0 560.0
Re: [gmx-users] Regarding mdrunfor small organic molecules
Ravi Kumar Venkatraman wrote: Dear All, When I try to grompp to generate .tpr file for mdrun from topology generated by prodrg I am getting the following error. Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'PRODRG' --- Program grompp_d, VERSION 4.5.4 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am herewith attaching the chlor.top file please help me findout the problem. You should always check the Gromacs site and mailing list archive first. This issue has come up hundreds of times and has a solution posted online: http://www.gromacs.org/Documentation/Errors#Fatal_error.3a_No_such_moleculetype_XXX Hint: you're missing an #include statement. -Justin ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; #include ffG43a1.itp [ moleculetype ] ; Name nrexcl PRODRG3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 O 1 PDB OAE 1 -0.6772 15.9994 2 C 1 PDB CAK 10.8450 12.0110 3 C 1 PDB CAG 10.0134 12.0110 4CL 1 PDBCLAA 1 -0.0968 35.4530 5 C 1 PDB CAH 20.0134 12.0110 6CL 1 PDBCLAB 2 -0.0968 35.4530 7 C 1 PDB CAL 20.8450 12.0110 8 O 1 PDB OAF 2 -0.6772 15.9994 9 C 1 PDB CAJ 20.0134 12.0110 10CL 1 PDBCLAD 2 -0.0968 35.4530 11 C 1 PDB CAI 20.0134 12.0110 12CL 1 PDBCLAC 3 -0.0968 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.123 1660.00.123 1660.0 ; CAK OAE 2 3 20.139 1080.00.139 1080.0 ; CAK CAG 2 11 20.139 1080.00.139 1080.0 ; CAK CAI 3 4 20.173 2928800.00.173 2928800.0 ; CAG CLAA 3 5 20.139 1080.00.139 1080.0 ; CAG CAH 5 6 20.173 2928800.00.173 2928800.0 ; CAH CLAB 5 7 20.139 1080.00.139 1080.0 ; CAH CAL 7 8 20.123 1660.00.123 1660.0 ; CAL OAF 7 9 20.139 1080.00.139 1080.0 ; CAL CAJ 9 10 20.173 2928800.00.173 2928800.0 ; CAJ CLAD 9 11 20.139 1080.00.139 1080.0 ; CAJ CAI 11 12 20.173 2928800.00.173 2928800.0 ; CAI CLAC [ pairs ] ; ai aj fuc0, c1, ... 1 4 1 ; OAE CLAA 1 5 1 ; OAE CAH 1 9 1 ; OAE CAJ 1 12 1 ; OAE CLAC 2 6 1 ; CAK CLAB 2 7 1 ; CAK CAL 2 10 1 ; CAK CLAD 3 8 1 ; CAG OAF 3 9 1 ; CAG CAJ 3 12 1 ; CAG CLAC 4 6 1 ; CLAA CLAB 4 7 1 ; CLAA CAL 4 11 1 ; CLAA CAI 5 10 1 ; CAH CLAD 5 11 1 ; CAH CAI 6 8 1 ; CLAB OAF 6 9 1 ; CLAB CAJ 7 12 1 ; CAL CLAC 8 10 1 ; OAF CLAD 8 11 1 ; OAF CAI 10 12 1 ; CLAD CLAC [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2121.0 685.0121.0 685.0 ; OAE CAK CAG 1 2 11 2121.0 685.0121.0 685.0 ; OAE CAK CAI 3 2 11 2120.0 560.0120.0 560.0 ; CAG CAK CAI 2 3 4 2120.0 560.0120.0 560.0 ; CAK CAG CLAA 2 3 5 2120.0 560.0120.0
[gmx-users] Re: Regarding mdrunfor small organic molecules
Dear all, Please can anybody send, step by step mdrun for small organic molecules in gromacs. Dear All, When I try to grompp to generate .tpr file for mdrun from topology generated by prodrg I am getting the following error. Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'PRODRG' --- Program grompp_d, VERSION 4.5.4 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype SOL For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am herewith attaching the chlor.top file please help me findout the problem. ; ; When using this software in a publication, cite: ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). ; PRODRG - a tool for high-throughput crystallography ; of protein-ligand complexes. ; Acta Crystallogr. D60, 1355--1363. ; ; #include ffG43a1.itp [ moleculetype ] ; Name nrexcl PRODRG3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 O 1 PDB OAE 1 -0.6772 15.9994 2 C 1 PDB CAK 10.8450 12.0110 3 C 1 PDB CAG 10.0134 12.0110 4CL 1 PDBCLAA 1 -0.0968 35.4530 5 C 1 PDB CAH 20.0134 12.0110 6CL 1 PDBCLAB 2 -0.0968 35.4530 7 C 1 PDB CAL 20.8450 12.0110 8 O 1 PDB OAF 2 -0.6772 15.9994 9 C 1 PDB CAJ 20.0134 12.0110 10CL 1 PDBCLAD 2 -0.0968 35.4530 11 C 1 PDB CAI 20.0134 12.0110 12CL 1 PDBCLAC 3 -0.0968 35.4530 [ bonds ] ; ai aj fuc0, c1, ... 2 1 20.123 1660.00.123 1660.0 ; CAK OAE 2 3 20.139 1080.00.139 1080.0 ; CAK CAG 2 11 20.139 1080.00.139 1080.0 ; CAK CAI 3 4 20.173 2928800.00.173 2928800.0 ; CAG CLAA 3 5 20.139 1080.00.139 1080.0 ; CAG CAH 5 6 20.173 2928800.00.173 2928800.0 ; CAH CLAB 5 7 20.139 1080.00.139 1080.0 ; CAH CAL 7 8 20.123 1660.00.123 1660.0 ; CAL OAF 7 9 20.139 1080.00.139 1080.0 ; CAL CAJ 9 10 20.173 2928800.00.173 2928800.0 ; CAJ CLAD 9 11 20.139 1080.00.139 1080.0 ; CAJ CAI 11 12 20.173 2928800.00.173 2928800.0 ; CAI CLAC [ pairs ] ; ai aj fuc0, c1, ... 1 4 1 ; OAE CLAA 1 5 1 ; OAE CAH 1 9 1 ; OAE CAJ 1 12 1 ; OAE CLAC 2 6 1 ; CAK CLAB 2 7 1 ; CAK CAL 2 10 1 ; CAK CLAD 3 8 1 ; CAG OAF 3 9 1 ; CAG CAJ 3 12 1 ; CAG CLAC 4 6 1 ; CLAA CLAB 4 7 1 ; CLAA CAL 4 11 1 ; CLAA CAI 5 10 1 ; CAH CLAD 5 11 1 ; CAH CAI 6 8 1 ; CLAB OAF 6 9 1 ; CLAB CAJ 7 12 1 ; CAL CLAC 8 10 1 ; OAF CLAD 8 11 1 ; OAF CAI 10 12 1 ; CLAD CLAC [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 2121.0 685.0121.0 685.0 ; OAE CAK CAG 1 2 11 2121.0 685.0121.0 685.0 ; OAE CAK CAI 3 2 11 2120.0 560.0120.0 560.0 ; CAG CAK CAI 2 3 4 2120.0 560.0120.0 560.0 ; CAK CAG CLAA 2 3 5 2120.0 560.0120.0 560.0 ; CAK CAG CAH 4 3 5 2120.0 560.0120.0 560.0 ; CLAA CAG CAH 3 5 6 2120.0 560.0120.0 560.0 ; CAG CAH CLAB 3 5 7 2120.0 560.0120.0 560.0 ; CAG
[gmx-users] Dear Lemkul
I could not find out what is wrong I tried add to add #include ions.itp and #ifdef but it is not successful. Fatal error: No such moleculetype SOL Please help me. I got stuck with this. Please. -- 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 mdrunfor small organic molecules
Ravi Kumar Venkatraman wrote: I could not find out what is wrong I tried add to add #include ions.itp and #ifdef but it is not successful. SOL is water, not ions. #include an appropriate water model. -Justin Fatal error: No such moleculetype SOL Please help me. I got stuck with this. Please. -- 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] Dear Lemkul
Hi Ravi, SOL does not sound like an ion to me. You probably want to include the topology for a water model, like spc.itp It sounds like you're trying things without knowing what, the way you mention #include and #ifdef. Did you try the tutorial material already? Cheers, Tsjerk On Aug 12, 2011 10:11 PM, Ravi Kumar Venkatraman ravikumarvenkatra...@gmail.com wrote: I could not find out what is wrong I tried add to add #include ions.itp and #ifdef but it is not successful. Fatal error: No such moleculetype SOL Please help me. I got stuck with this. Please. -- 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] Viscosity units
Dear gmx-users, I am trying to learn viscosity calculations using non-equilibrium method in Gromacs 4.5.4. I have gone through Hess paper and several posts on viscosity calculation. I have setup a system of pure water (32000 molecules) and run till 10 ns using NPT and setting cos-acceleration=0.1 nm/ps^2 in .mdp file. Then, I have used following command to get viscosity from energy file. g_energy_d -f .edr -s .tpr -o energy.xvg and selected 1/viscosity from one of the options and I get, Energy Average Err.Est. RMSD Tot-Drift --- 1/Viscosity 1.64374 0.0016 0.0341615 0.00789197 (m s/kg) This gives Viscosity=1/1.64374= 0.6083 kg/ms=608.3 cP I have some doubts regarding this result: 1) Can anyone please tell me what are the units of viscosity here. It shows from screen output (as well from energy.xvg) that 1/viscosity is in m-s/kg units. But, the experimental value for pure water is 0.854 cP =0.000854 kg/m-s. So, I have a doubt regarding units coming from GROMACS it is in cP or kg/m-s as printed. If kg/ms are the units then, this value of viscosity for pure water is not correct ? Please tell me what I am doing wrong here. 2) Is this a right way of calculating viscosity using NEMD or I should do it by using 2CosZ*Vel-X option. Please tell me how can I get viscosity from this term. Any suggestions/comments are most welcome. Thanks and Regards, Dr. Rini Gupta UBC, Vancouver -- 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] how to simulate a line charge
Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. Thanks -- 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] how to simulate a line charge
Amit Choubey wrote: Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp If you're trying to keep the atoms in a line, the system will not be stable. Angles of 180 degrees routinely crash. files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. The maximum charge group size is defined in the include/types/nblist.h header. You can alter the value there, which will get around the error, but consider whether or not this is even a good physical model. If all atoms are in the same charge group, there are no electrostatic interactions between these atoms since neighbor searching is done and short-range energies are calculated based on inter-charge group distances. I have no idea how to properly simulate a line of positively-charged particles, but be aware. -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] how to simulate a line charge
On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp If you're trying to keep the atoms in a line, the system will not be stable. Angles of 180 degrees routinely crash. Not even if i use a 3 body angle term with equilibrium angle = 180? If not then why ? files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. The maximum charge group size is defined in the include/types/nblist.h header. You can alter the value there, which will get around the error, but consider whether or not this is even a good physical model. If all atoms are in the same charge group, there are no electrostatic interactions between these atoms since neighbor searching is done and short-range energies are calculated based on inter-charge group distances. I have no idea how to properly simulate a line of positively-charged particles, but be aware. Thanks for the pointer and the awareness remark. But since this is a model system and for the physical problem i am trying to deal with its alright if the atoms within the line charge do not interact via non-bonded potentials. -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/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] how to simulate a line charge
Amit Choubey wrote: On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp If you're trying to keep the atoms in a line, the system will not be stable. Angles of 180 degrees routinely crash. Not even if i use a 3 body angle term with equilibrium angle = 180? If not then why ? The code has had problems dealing with this case. I do not know if there have been any improvements. The only really stable way to induce linearity is through virtual sites, but I don't know if it is possible to create several hundred virtual interactions defined along a line. -Justin files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/__Documentation/Errors http://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. The maximum charge group size is defined in the include/types/nblist.h header. You can alter the value there, which will get around the error, but consider whether or not this is even a good physical model. If all atoms are in the same charge group, there are no electrostatic interactions between these atoms since neighbor searching is done and short-range energies are calculated based on inter-charge group distances. I have no idea how to properly simulate a line of positively-charged particles, but be aware. Thanks for the pointer and the awareness remark. But since this is a model system and for the physical problem i am trying to deal with its alright if the atoms within the line charge do not interact via non-bonded potentials. -Justin -- ==__== 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 tel:%28540%29%20231-9080 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
